07.14.17
This week has been filled with poster finalizations and now they are submitted for Prague next week. DNA was extracted from different samples of UMB901 and about half worked, but the DNA was fragmented. However that is still DNA! I'll be brainstorming about how to get complete DNA from 901. Also we found a strange host range for this phage. A phage that plaqued on EcB then harvested and replated on EcC, will not replate on EcB when harvested from the EcC plate. The same situation is being seen for a phage that plaqued on K12. I am unsure of why this is happening, and it is another phenomenon that will have to be brainstormed. Finally, next Wednesday we leave for Prague and I'm excited to present virMine.
This week has been filled with poster finalizations and now they are submitted for Prague next week. DNA was extracted from different samples of UMB901 and about half worked, but the DNA was fragmented. However that is still DNA! I'll be brainstorming about how to get complete DNA from 901. Also we found a strange host range for this phage. A phage that plaqued on EcB then harvested and replated on EcC, will not replate on EcB when harvested from the EcC plate. The same situation is being seen for a phage that plaqued on K12. I am unsure of why this is happening, and it is another phenomenon that will have to be brainstormed. Finally, next Wednesday we leave for Prague and I'm excited to present virMine.
07.10.17
It's been a busy but exciting time in the lab! We're plating UMB901 on different hosts and getting decent concentrations to be able to do DNA extractions that can be sent out for sequencing hopefully this week. We have also run different samples through virMine including some from Lake Michigan, the gut, and urine. The results have come back and we're pretty happy with how the program is working; it is even finding prophages. This data is being incorporated into my poster for the International Bioinformatics conference in Prague. We leave for Prague in a little over a week and things seem to be coming together nicely to put together an informative poster! I'm getting excited to complete it and be able to present the work I have done all year.
It's been a busy but exciting time in the lab! We're plating UMB901 on different hosts and getting decent concentrations to be able to do DNA extractions that can be sent out for sequencing hopefully this week. We have also run different samples through virMine including some from Lake Michigan, the gut, and urine. The results have come back and we're pretty happy with how the program is working; it is even finding prophages. This data is being incorporated into my poster for the International Bioinformatics conference in Prague. We leave for Prague in a little over a week and things seem to be coming together nicely to put together an informative poster! I'm getting excited to complete it and be able to present the work I have done all year.
06.19.17
This past week we have been running our various test samples through virMine and, although not all are finished yet, we are pretty happy with the results from the finished samples. I have also been working on a script for remote blasting so we can get some statistics on the accuracy of virMine. On the benchtop I have been doing some more work with UMB901 by plating on different E. coli hosts and trying to get a higher concentration. Hopefully if we can obtain a high concentration of phage we will be able to perform a successful DNA extraction which we can send out for sequencing. We have also discovered that UMB901 plates successfully on E.coli C and E.coli B. Furthermore, we know that two other bladder E. coli bacteria, UMB900 and UMB789, contain prophages which we are trying to isolate. These seem to be a little trickier and we will have to find different ways to stress the host and get the phages to come out. Lastly, we have finally seen 901 plaque on E.coli K12. They were few and faint plaques but we harvested them and will re-plate to see if we can get a clearer lawn. It's possible that different hosts encourage lysis of different phages, or one phage has obtained a slight mutation allowing it to plate on multiple hosts. We will be isolating plaques from the various hosts and sending out for sequencing to see what we find.
This past week we have been running our various test samples through virMine and, although not all are finished yet, we are pretty happy with the results from the finished samples. I have also been working on a script for remote blasting so we can get some statistics on the accuracy of virMine. On the benchtop I have been doing some more work with UMB901 by plating on different E. coli hosts and trying to get a higher concentration. Hopefully if we can obtain a high concentration of phage we will be able to perform a successful DNA extraction which we can send out for sequencing. We have also discovered that UMB901 plates successfully on E.coli C and E.coli B. Furthermore, we know that two other bladder E. coli bacteria, UMB900 and UMB789, contain prophages which we are trying to isolate. These seem to be a little trickier and we will have to find different ways to stress the host and get the phages to come out. Lastly, we have finally seen 901 plaque on E.coli K12. They were few and faint plaques but we harvested them and will re-plate to see if we can get a clearer lawn. It's possible that different hosts encourage lysis of different phages, or one phage has obtained a slight mutation allowing it to plate on multiple hosts. We will be isolating plaques from the various hosts and sending out for sequencing to see what we find.
06.05.17
We have been accepted to present our VirMine poster at the ISMB/ECCB 2017 conference in Prague at the end of July.
In the lab, I started new cultures to isolate phage. We have completed all benchmarking for VirMine and began processing several real samples including viral metagenomic data sets from two freshwater lakes, samples from the human gut microbiota, and samples from the human bladder microbiota. Computations for the freshwater lake data sets are complete and the human microbiota sequencing reads are presently being processed. This week I'll begin analyses of the results generated by VirMine. This week the lab is also doing two workshops, one in Scientific Writing and another in Python.
We have been accepted to present our VirMine poster at the ISMB/ECCB 2017 conference in Prague at the end of July.
In the lab, I started new cultures to isolate phage. We have completed all benchmarking for VirMine and began processing several real samples including viral metagenomic data sets from two freshwater lakes, samples from the human gut microbiota, and samples from the human bladder microbiota. Computations for the freshwater lake data sets are complete and the human microbiota sequencing reads are presently being processed. This week I'll begin analyses of the results generated by VirMine. This week the lab is also doing two workshops, one in Scientific Writing and another in Python.
05.21.17
This past week we attended the Great Lake Bioinformatics conference and I presented my poster about VirMine. It was a three day conference where we attended various talks on the microbiome and new techniques on studying the microscopic beings that control so much of our lives. We also attended talks on different computational tools being used to analyze data. On the third day I presented my poster and I think it went pretty well. I talked to various lab directors and one guy from the Mayo Clinic, and people seemed to be very interested in the pipeline. Next we will be adding new results to the poster and we test on real data sets.
This past week we attended the Great Lake Bioinformatics conference and I presented my poster about VirMine. It was a three day conference where we attended various talks on the microbiome and new techniques on studying the microscopic beings that control so much of our lives. We also attended talks on different computational tools being used to analyze data. On the third day I presented my poster and I think it went pretty well. I talked to various lab directors and one guy from the Mayo Clinic, and people seemed to be very interested in the pipeline. Next we will be adding new results to the poster and we test on real data sets.
05.13.17
To kick off the summer some of my fellow lab mates and I volunteered at an event to teach kids about STEM fields. There were many different tables including the use of a pendulum to make art and the chance to make your own helicopter. Our booth was making a monster according to a genetic code. There were four differently colored legos representing the four DNA bases. The kids would pick eight random blocks that corresponded to eight characteristics for their monster including things like number of eyes and body shape. Each color gave a different answer in the categories such as a triangle, square, circle, or rectangle body depending on the color. Then the kids got to use crayons, pipe-cleaners, pom-poms, and googly eyes to create their monster. There was a large turn out of kids and they had fun making their own unique monster. It was also fun for us to help the kids and get them interested in STEM!
To kick off the summer some of my fellow lab mates and I volunteered at an event to teach kids about STEM fields. There were many different tables including the use of a pendulum to make art and the chance to make your own helicopter. Our booth was making a monster according to a genetic code. There were four differently colored legos representing the four DNA bases. The kids would pick eight random blocks that corresponded to eight characteristics for their monster including things like number of eyes and body shape. Each color gave a different answer in the categories such as a triangle, square, circle, or rectangle body depending on the color. Then the kids got to use crayons, pipe-cleaners, pom-poms, and googly eyes to create their monster. There was a large turn out of kids and they had fun making their own unique monster. It was also fun for us to help the kids and get them interested in STEM!
04.21.17
We are winding down to the last two weeks of the semester. This upcoming week (which will be my last week in the lab until finals are over) I will continue putting my poster together for the GLBio conference as well as testing virMine and isolating my phages. The last plate I had showed two different morphologies, one clear and one blurry, so today I will be picking both these plaques, re-plating them to see the morphologies, and performing a DNA extraction, seeing what the bands look like, and drawing conclusions from there. Next week I will re-plate the plaque picks on E.coli C and K12 and seeing what the morphologies look like. Next week we will also be running the test data sets through VirMine and then the real data sets so we have some results to report on how the pipeline works.
We are winding down to the last two weeks of the semester. This upcoming week (which will be my last week in the lab until finals are over) I will continue putting my poster together for the GLBio conference as well as testing virMine and isolating my phages. The last plate I had showed two different morphologies, one clear and one blurry, so today I will be picking both these plaques, re-plating them to see the morphologies, and performing a DNA extraction, seeing what the bands look like, and drawing conclusions from there. Next week I will re-plate the plaque picks on E.coli C and K12 and seeing what the morphologies look like. Next week we will also be running the test data sets through VirMine and then the real data sets so we have some results to report on how the pipeline works.
04.14.17
Wow so much has been happing these past few weeks! We discovered two different phage morphologies from the bladder E.coli; one from a sample I cultivated and one from our post-doc. I've been going back and forth trying to isolate the different morphologies, but it seems that while the clear plaques show up consistently, the bulls-eye plaques are a little less consistent. Both plaque morphologies came from both samples though my sample seemed to give more clear plaques. I can get plates with a lot of clear and a couple bulls-eye, and plates with a lot of bulls-eye and a couple clear. I've also been getting plaques that have been consistently clear and then as I continue plaque purification, a bulls-eye shows up. Something during the plating process is causing one phage to come out over the other; this could be due to things like the heat of the soft agar, or the time the phage sits with the bacteria before being plated, or the amount of time the sample is in the fridge. The process of discovering how to get consistent plaques has not been easy or short. I've spent weeks plating and having some bumps in the road. But thats research! Search and if you don't find anything, re-search again.
However, work on VirMine has had significant progress. The code is almost ready to be tested on the practice data sets I put together using the program MetaSim. We are also starting to submit abstracts for different conferences. We're planning on submitting an abstract for consideration for a short talk for the international computational biology conference in Prague in July. As my last blog entry mentioned, I'll be presenting my work at GLBio. I'll be working on making a poster for the GLBio as well as working on submissions for the conference in Prague in the week to come. Furthermore, I will be continuing on trying to the isolate two different phages!
Wow so much has been happing these past few weeks! We discovered two different phage morphologies from the bladder E.coli; one from a sample I cultivated and one from our post-doc. I've been going back and forth trying to isolate the different morphologies, but it seems that while the clear plaques show up consistently, the bulls-eye plaques are a little less consistent. Both plaque morphologies came from both samples though my sample seemed to give more clear plaques. I can get plates with a lot of clear and a couple bulls-eye, and plates with a lot of bulls-eye and a couple clear. I've also been getting plaques that have been consistently clear and then as I continue plaque purification, a bulls-eye shows up. Something during the plating process is causing one phage to come out over the other; this could be due to things like the heat of the soft agar, or the time the phage sits with the bacteria before being plated, or the amount of time the sample is in the fridge. The process of discovering how to get consistent plaques has not been easy or short. I've spent weeks plating and having some bumps in the road. But thats research! Search and if you don't find anything, re-search again.
However, work on VirMine has had significant progress. The code is almost ready to be tested on the practice data sets I put together using the program MetaSim. We are also starting to submit abstracts for different conferences. We're planning on submitting an abstract for consideration for a short talk for the international computational biology conference in Prague in July. As my last blog entry mentioned, I'll be presenting my work at GLBio. I'll be working on making a poster for the GLBio as well as working on submissions for the conference in Prague in the week to come. Furthermore, I will be continuing on trying to the isolate two different phages!
04.02.17
My abstract was accepted for a poster at GLBio - the Great Lakes Bioinformatics Conference. This will be my first poster presentation!
My abstract was accepted for a poster at GLBio - the Great Lakes Bioinformatics Conference. This will be my first poster presentation!
02.28.17
This week is midterms & next week is spring break. Lots of studying so I won't likely be able to get any research work done until I come back from spring break.
This week is midterms & next week is spring break. Lots of studying so I won't likely be able to get any research work done until I come back from spring break.
02.24.17
In the lab, the DNA extraction was successful. We possibly have identified two phages from the bladder E. coli; one that I have identified and one our post-doc Jason has identified. I will be spotting both phage lysates on the same E. coli C lawns and comparing plaque morphology. As for our software development, we've made some progress with debugging some of the code and adding more meaningful error messages for the user. We have our first beta-testers lined up - Dr. Siv Watkins' lab at New Mexico Tech. We're hoping to get the code to them this week (after improving the comments in the code). This last week and upcoming week I have midterms so I have not been getting as much done as I would like too. I'm hoping for more progress after spring break.
In the lab, the DNA extraction was successful. We possibly have identified two phages from the bladder E. coli; one that I have identified and one our post-doc Jason has identified. I will be spotting both phage lysates on the same E. coli C lawns and comparing plaque morphology. As for our software development, we've made some progress with debugging some of the code and adding more meaningful error messages for the user. We have our first beta-testers lined up - Dr. Siv Watkins' lab at New Mexico Tech. We're hoping to get the code to them this week (after improving the comments in the code). This last week and upcoming week I have midterms so I have not been getting as much done as I would like too. I'm hoping for more progress after spring break.
02.20.17
PCR reactions to amplify the phage DNA were unsuccessful. This week I will re-extract DNA from the phage lysate and try the PCR reaction again. I will also be implementing revisions and comments that were made to the virMine paper. At our lab meeting I presented a paper "Bacteriophages as potential treatment for Urinary Tract Infections" (PMC 4826877). This paper is related to my work in the laboratory working with phages from the bladder. Here they were testing the use of phages to treat UTIs in the bladder. This week I learned a lot about PCR trouble-shooting (which I hope will be successful soon) and the possible medical uses of phages (from the paper I presented).
PCR reactions to amplify the phage DNA were unsuccessful. This week I will re-extract DNA from the phage lysate and try the PCR reaction again. I will also be implementing revisions and comments that were made to the virMine paper. At our lab meeting I presented a paper "Bacteriophages as potential treatment for Urinary Tract Infections" (PMC 4826877). This paper is related to my work in the laboratory working with phages from the bladder. Here they were testing the use of phages to treat UTIs in the bladder. This week I learned a lot about PCR trouble-shooting (which I hope will be successful soon) and the possible medical uses of phages (from the paper I presented).
02.13.17
The figure on the right describes the flow of our pipeline virMine. Step one accepts QC raw reads and performs De novo assembly. The (optional) second step is to filter the contigs. From here the contigs go through open reading frame prediction. Then each contig is compared to specifically curated viral and non-viral databases. Finally virMine returns putative viral contigs with annotations. I am currently working on revisions on the virMine research paper as well as further work to extract DNA from the bladder phage. After a restriction enzyme digest we believe we have identified a phage. Future work will consist of characterizing this phage and annotating its genome. |
02.06.17
As we continue work on the pipeline, I worked on writing a script that will check the user's computer to make sure each of the programs included in virMine are in the PATH variable. Our pipeline requires that tools are included in PATH so the pipeline doesn't have to know the location of the tools on the users machine. If the user does not have one of the programs added to the PATH, the user is alerted and prompted to add the program's path to the PATH variable. The pipeline won't try to run and fail because it cannot run one of the programs. We have put together a list, with links, of the programs our pipeline uses. When a new user installs our pipeline they first have to install GLIMMER, sickle, SPAdes, MEGAhit, and their dependencies. The function I wrote this week checks that everything is installed correctly.
I have also extracted DNA from the phage from the bladder bacteria and am working on making primers for a PCR reaction to amplify the DNA. My goals going forward are to amplify the phage DNA and sequence it so we can test virMine using this data. Also, I will be working further on cleaning up the pipeline.
As we continue work on the pipeline, I worked on writing a script that will check the user's computer to make sure each of the programs included in virMine are in the PATH variable. Our pipeline requires that tools are included in PATH so the pipeline doesn't have to know the location of the tools on the users machine. If the user does not have one of the programs added to the PATH, the user is alerted and prompted to add the program's path to the PATH variable. The pipeline won't try to run and fail because it cannot run one of the programs. We have put together a list, with links, of the programs our pipeline uses. When a new user installs our pipeline they first have to install GLIMMER, sickle, SPAdes, MEGAhit, and their dependencies. The function I wrote this week checks that everything is installed correctly.
I have also extracted DNA from the phage from the bladder bacteria and am working on making primers for a PCR reaction to amplify the DNA. My goals going forward are to amplify the phage DNA and sequence it so we can test virMine using this data. Also, I will be working further on cleaning up the pipeline.
01.20.17
My recent work has consisted of creating a pipeline, named virMine, to filter through metagenomic data sets and identify viral samples. First this pipeline takes in raw reads, trims using Sickle, and assembles using SPAdes, metaSPAdes, or MEGAhit. Next is an optional step to filter the contigs. Following this the contigs are passed to GLIMMER for open reading frame (ORF) prediction. Finally each predicted ORF is compared to two databases – a collection of non-viral sequences and known viral sequences. This is completed using blastx. All hits are reported to both databases and the bitscores are compared to assess the likelihood that the ORF is viral. virMine outputs two files, one consisting of predicted viral ORFs, and the other of non-viral ORFs. For this pipeline I specifically worked with GLIMMER, creating a script using python to convert the output file from SPAdes into a file that can be accepted and run through GLIMMER. I also worked with the script for blastx and determining if a contig was viral or non-viral.
I have been working on writing a paper to present this pipeline. My goals going forward are to clean up the pipeline and test it using real data sets, and also work more on the paper for virMine. Lastly, I am working on extracting phage DNA from E.coli bacteria isolated from the bladder. This data will be useful to test using virMine.
My recent work has consisted of creating a pipeline, named virMine, to filter through metagenomic data sets and identify viral samples. First this pipeline takes in raw reads, trims using Sickle, and assembles using SPAdes, metaSPAdes, or MEGAhit. Next is an optional step to filter the contigs. Following this the contigs are passed to GLIMMER for open reading frame (ORF) prediction. Finally each predicted ORF is compared to two databases – a collection of non-viral sequences and known viral sequences. This is completed using blastx. All hits are reported to both databases and the bitscores are compared to assess the likelihood that the ORF is viral. virMine outputs two files, one consisting of predicted viral ORFs, and the other of non-viral ORFs. For this pipeline I specifically worked with GLIMMER, creating a script using python to convert the output file from SPAdes into a file that can be accepted and run through GLIMMER. I also worked with the script for blastx and determining if a contig was viral or non-viral.
I have been working on writing a paper to present this pipeline. My goals going forward are to clean up the pipeline and test it using real data sets, and also work more on the paper for virMine. Lastly, I am working on extracting phage DNA from E.coli bacteria isolated from the bladder. This data will be useful to test using virMine.
12.05.16
'VirusTAP: Viral Genome-Targeted Assembly Pipeline' describes the method of viral genome assembly as performed by the pipeline VirusTAP. This pipeline begins by trimming the sequence from the 5'-end and removing the adapter. Next is read subtraction, which is performed in two steps. First the reads are mapped to rRNA sequences, bacterial genomes, and virus-host genomes using the bwasw program. Next non-virus reads are eliminated by filtering against a viral nucleotide/protein database. Following this the reads are assembled using one of four de novo assembly pipelines: A5-miseq, Platanus with PriceTI, IDBA-UD with PrideTI, and SPAdes. Finally a blastn homology search is performed for each of the reads.
'VirusTAP: Viral Genome-Targeted Assembly Pipeline' describes the method of viral genome assembly as performed by the pipeline VirusTAP. This pipeline begins by trimming the sequence from the 5'-end and removing the adapter. Next is read subtraction, which is performed in two steps. First the reads are mapped to rRNA sequences, bacterial genomes, and virus-host genomes using the bwasw program. Next non-virus reads are eliminated by filtering against a viral nucleotide/protein database. Following this the reads are assembled using one of four de novo assembly pipelines: A5-miseq, Platanus with PriceTI, IDBA-UD with PrideTI, and SPAdes. Finally a blastn homology search is performed for each of the reads.
11.25.16
'Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR' compares the techniques of bioinformatics screening and PCR in detecting viruses in the bloodstream. Bioinformatic screening of metagenomic sequence libraries has the advantage of detecting a wide variety of genomic variants that would require multiple individual PCRs for the same result. Bioinformatic screening can also assemble near-complete genomes for the virus in question. PCR results are normally short amplicons that provide much less information than the genomic sequences from bioinformatic screening. A drawback of bioinformatic screening is that is dependent on the quality of the library. If the library contains contamination sequences, results screening from this library will not be accurate. PCRs are capable of single copy target sensitivity and can therefore avoid false-positives from contamination.
From this paper, it seems that bioinformatic screening is the best way to determine viral components. As long as care is taken to be sure the library is free of contaminants, using a metagenomic library would be the most efficient process.
'Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR' compares the techniques of bioinformatics screening and PCR in detecting viruses in the bloodstream. Bioinformatic screening of metagenomic sequence libraries has the advantage of detecting a wide variety of genomic variants that would require multiple individual PCRs for the same result. Bioinformatic screening can also assemble near-complete genomes for the virus in question. PCR results are normally short amplicons that provide much less information than the genomic sequences from bioinformatic screening. A drawback of bioinformatic screening is that is dependent on the quality of the library. If the library contains contamination sequences, results screening from this library will not be accurate. PCRs are capable of single copy target sensitivity and can therefore avoid false-positives from contamination.
From this paper, it seems that bioinformatic screening is the best way to determine viral components. As long as care is taken to be sure the library is free of contaminants, using a metagenomic library would be the most efficient process.
11.05.16
One of the more recent viral identification tools is CRISPRs. CRISPRs have developed as bacterial phage resistance mechanism. Bacteria incorporate viral DNA into CRISPRs as spacers in their own genomes. Presence of these spacers in the bacterial genome gives the bacteria resistance against phages containing the same sequence. These sequences help us to identify viruses because by locating the CRISPR sequence from the bacteria we can discover a phage's host after matching the CRISPR sequence to a virus (18497291). Also, putting together a viral gene database from sources such as NCBI database (BLAST and RefSeq) and Phage Orthologous Groups (POGs-07-inf.pq) database (26191051) will give us an index to compare our unknown sequences to.
One of the more recent viral identification tools is CRISPRs. CRISPRs have developed as bacterial phage resistance mechanism. Bacteria incorporate viral DNA into CRISPRs as spacers in their own genomes. Presence of these spacers in the bacterial genome gives the bacteria resistance against phages containing the same sequence. These sequences help us to identify viruses because by locating the CRISPR sequence from the bacteria we can discover a phage's host after matching the CRISPR sequence to a virus (18497291). Also, putting together a viral gene database from sources such as NCBI database (BLAST and RefSeq) and Phage Orthologous Groups (POGs-07-inf.pq) database (26191051) will give us an index to compare our unknown sequences to.
10.28.16
Unfortunately this week has been slightly more difficult for me to make progress due to my recent concussion. I am slowly developing the introduction our research paper.
Unfortunately this week has been slightly more difficult for me to make progress due to my recent concussion. I am slowly developing the introduction our research paper.
10.20.16
How to determine if a gene is viral:
First is the presence of no bacteria housekeeping genes. Bacteria have their own set of genes that keep the cell alive. This includes genes for DNA transcription and translation, the bacteria identifying 16S gene, cell wall and structure genes, and many more. There are also some genes specific to viruses that help with identification. This includes capsid, tail, and baseplate protein genes, terminase (used in DNA packing mechanisms), portal protein (viral chromosome packing), and tape measure protein (length of phage tail).
CRISPRs have developed as bacterial phage resistance mechanism. Bacteria incorporate viral DNA into CRISPRs as spacers in their own genomes. Presence of these spacers in the bacterial genome gives the bacteria resistance against phages containing the same sequence. These sequences help us to identify viruses because by locating the CRISPR sequence from the bacteria we can discover a phage's host after matching the CRISPR sequence to a virus.
We will also be creating a database of all metaviral analyses to compare our sequences to. This will include sequences from NCBI using BLAST and RefSeq, as well as the database of Phage Orthologous Groups (POGs).
How to determine if a gene is viral:
First is the presence of no bacteria housekeeping genes. Bacteria have their own set of genes that keep the cell alive. This includes genes for DNA transcription and translation, the bacteria identifying 16S gene, cell wall and structure genes, and many more. There are also some genes specific to viruses that help with identification. This includes capsid, tail, and baseplate protein genes, terminase (used in DNA packing mechanisms), portal protein (viral chromosome packing), and tape measure protein (length of phage tail).
CRISPRs have developed as bacterial phage resistance mechanism. Bacteria incorporate viral DNA into CRISPRs as spacers in their own genomes. Presence of these spacers in the bacterial genome gives the bacteria resistance against phages containing the same sequence. These sequences help us to identify viruses because by locating the CRISPR sequence from the bacteria we can discover a phage's host after matching the CRISPR sequence to a virus.
We will also be creating a database of all metaviral analyses to compare our sequences to. This will include sequences from NCBI using BLAST and RefSeq, as well as the database of Phage Orthologous Groups (POGs).
10.14.16
This week I started writing a few paragraphs summarizing the information on tools to identify viral genes. I have also started learning python coding for our future pipeline.
This week I started writing a few paragraphs summarizing the information on tools to identify viral genes. I have also started learning python coding for our future pipeline.
10.06.2016
Research articles I have read through include 'Analysis of Virus Genomes from Glacial Environments Reveals Novel Virus Groups with Unusual Host Interactions' (PubMed reference number 26191051), 'Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities' (18497291), and 'Expanding the Marine Virosphere Using Metagenomics' (24348267). Now armed with the information from these studies, I can start the beginnings of the paper we will use to present our research.
Research articles I have read through include 'Analysis of Virus Genomes from Glacial Environments Reveals Novel Virus Groups with Unusual Host Interactions' (PubMed reference number 26191051), 'Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities' (18497291), and 'Expanding the Marine Virosphere Using Metagenomics' (24348267). Now armed with the information from these studies, I can start the beginnings of the paper we will use to present our research.
10.05.2016
After reading through multiple studies done with viruses, I have come up with a general idea of all the ways viral genomes are identified. This list includes size of the genome, locating a specifically known viral gene, such as tail proteins or tape measure proteins, and the absence of bacterial housekeeping genes. Also, the presence of CRISPRs and Cas proteins in our bacterial sample can allow us to determine a viruses bacterial host. Putting together databases of genes from metaviromes, including sequences such as POGs, to search sequences against is another common technique, something that we of no doubt be helpful in our project.
After reading through multiple studies done with viruses, I have come up with a general idea of all the ways viral genomes are identified. This list includes size of the genome, locating a specifically known viral gene, such as tail proteins or tape measure proteins, and the absence of bacterial housekeeping genes. Also, the presence of CRISPRs and Cas proteins in our bacterial sample can allow us to determine a viruses bacterial host. Putting together databases of genes from metaviromes, including sequences such as POGs, to search sequences against is another common technique, something that we of no doubt be helpful in our project.
09.22.2016
These past couple weeks I have been reading through multiple papers all dealing with viruses. In these papers I was looking specifically for the tools they used to confirm viral genomes. One of the criteria used was looking for phage specific genes such as those encoding for tail proteins, tape measure proteins, and the terminase gene essential for head-tail phages. The presence of important phage genes identified from Phage Orthologous Groups, and reads that matched viral CRISPER sequences were other identification tools considered. Lastly, using NCBI's BLAST to compare reads to already known viral sequences was a common technique, though not everything in the BLAST database is 100% accurate which calls the need for other tools of identification.
These past couple weeks I have been reading through multiple papers all dealing with viruses. In these papers I was looking specifically for the tools they used to confirm viral genomes. One of the criteria used was looking for phage specific genes such as those encoding for tail proteins, tape measure proteins, and the terminase gene essential for head-tail phages. The presence of important phage genes identified from Phage Orthologous Groups, and reads that matched viral CRISPER sequences were other identification tools considered. Lastly, using NCBI's BLAST to compare reads to already known viral sequences was a common technique, though not everything in the BLAST database is 100% accurate which calls the need for other tools of identification.
09.16.2016
Welcome to my research blog. This year funding for my research is provided by CREU. Follow my blog throughout the year as myself, as well as my partner Alexandria Miley and our faculy director Dr. Catherine Putonti dive into the the world of viral genomics. As a science community we know very little about this vastly abundant microorganism. Our goal this year is to use computer science to disover/create a better method of identifying viral genomes. An accurate database of viral genomes will push the current boundries of research that can be done with viruses and bacteriophages.
Welcome to my research blog. This year funding for my research is provided by CREU. Follow my blog throughout the year as myself, as well as my partner Alexandria Miley and our faculy director Dr. Catherine Putonti dive into the the world of viral genomics. As a science community we know very little about this vastly abundant microorganism. Our goal this year is to use computer science to disover/create a better method of identifying viral genomes. An accurate database of viral genomes will push the current boundries of research that can be done with viruses and bacteriophages.