User: Chrispin Chaguza

Reputation:
220
Status:
Trusted
Location:
University of Liverpool, UK
Website:
https://www.liv.ac.uk/...
Twitter:
ChrispinChaguza
Last seen:
1 year, 3 months ago
Joined:
3 years, 2 months ago
Email:
C***************@gmail.com

I'm a Commonwealth PhD Scholar in Infection and Immunity (Bioinformatics) at the Institute of Infection and Global Health, University of Liverpool, United Kingdom.

Posts by Chrispin Chaguza

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Recommended biology/genomics book for computer scientist students
... Attwood, Teresa K.; Higgs, Paul (2005). Bioinformatics And Molecular Evolution. Cambridge, MA: Blackwell Publishers. ISBN 1-4051-0683-2. ...
written 2.3 years ago by Chrispin Chaguza220
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Answer: A: virulence factor of a bacteria
... You could align the sequences for the virulence factor(s) of interest and construct a maximum likelihood phylogenetic tree. If you have metadata (phenotypic data etc) for the organisms from which the sequences were obtained, you could overlay these on the tree and see if you can observe some pattern ...
written 2.3 years ago by Chrispin Chaguza220
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Answer: A: Multiple whole genome alignment
... For that many bacterial genomes, whole genome alignment would either be impractical or might take very long time and require lots of computational resources to properly align them especially if working with a species that has high rates of genetic recombination/horizontal gene transfer such as Strep ...
written 2.3 years ago by Chrispin Chaguza220
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Answer: A: Whole Genome Snp And Core Genome Snp
... You could use snp_sites to find polymorphic sites (SNPs) in your whole genome alignments https://github.com/sanger-pathogens/snp_sites. I have created a basic analysis pipeline (http://mcgp.sourceforge.net/) that create alignments based on the whole genome content that's conserved between all strai ...
written 2.8 years ago by Chrispin Chaguza220
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Answer: A: Whole Genome Phylogeny
... It's a very old post but I thought I could add to it to help others who might want to do a similar analysis i.e. create phylogenies from whole genomes for prokaryotic species. I have created a basic analysis pipeline that tries to simplify the process of creating phylogenetic trees at species level ...
written 2.8 years ago by Chrispin Chaguza220
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Answer: A: Phylogenetic Analysis Of Whole Genomes
... It's a very old post but I thought I could add to it to help others who might want to do a similar analysis i.e. create phylogenies from whole genomes for prokaryotic species. I have created a basic analysis pipeline that tries to simplify the process of creating phylogenetic trees at species level ...
written 2.8 years ago by Chrispin Chaguza220
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Answer: A: Comparing two or more genomes for novel regions
... You could use ACT (https://www.sanger.ac.uk/resources/software/act/) to compare multiple genomes (or genomic regions) to identify unique regions. You could also use OrthoMCL (http://bit.ly/1EZPFYm) to identify unique regions (genes) in your species genomes. Here is an example of how genome comparis ...
written 2.9 years ago by Chrispin Chaguza220
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Answer: A: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
... Here is python script that can also be used to download GenBank files given accession numbers. Copy the python code below and save it as fetch_accession.py. Create a text file and give it a name say accessions.txt. Write these accession numbers (AP010935.1, AE014074.1, CP001129.1) to the file and s ...
written 2.9 years ago by Chrispin Chaguza220
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Answer: A: what is the best place to find latest phd positions in computational biology esp
... Probably a good idea to check on websites for various research groups that you would like to work with. You could also ask your Professors to recommend some good groups relevant to your expertise for you. Below are some good PhD studentships in genomics and bioinformatics that I know; https://www.s ...
written 2.9 years ago by Chrispin Chaguza220
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Answer: A: How To Get Conservation Of Vaccine Candidates Between Hundreds Of Bacterial Stra
... Do you also have whole genome sequences for the isolates? If yes, perhaps you could first do a core genome analysis to determine orthologous genes present in all the bacterial isolates. Ideally, a candidate gene for protein based vaccines should be in the 'core genome' i.e. present in all the bacter ...
written 3.0 years ago by Chrispin Chaguza220

Latest awards to Chrispin Chaguza

Appreciated 2.8 years ago, created a post with more than 5 votes. For A: What are the biggest challenges bioinformaticians have with data analysis?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What are the biggest challenges bioinformaticians have with data analysis?
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.

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