User: Brett

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Brett130
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130
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2 years, 5 months ago
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7 years ago
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Posts by Brett

<prev • 17 results • page 1 of 2 • next >
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Answer: A: PhD programs in bioinformatics and genomics
... The academic year has already started in the UK, and this is when most PhD students start. However there are continually positions offered throughout the year. I would personally recommend Edinburgh, however Imperial, York and Cambridge are excellent. The best site to check in the UK is www.job ...
written 2.4 years ago by Brett130
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Comment: C: Commercial software platform for stotage of omics data and basic analysis by sci
... I should add the data comes from bacterial genomes ...
written 2.4 years ago by Brett130
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Commercial software platform for stotage of omics data and basic analysis by scientists
... I am looking for a software solution for team of 20 scientists of various disciplines. In short we are generating omics data (Genome sequences, Metabolomics, RNA sequencing) and I want the scientists to have access to this data to do basic analysis themselves (BLAST, Genome comparisons, compare exp ...
omics data storage data visualisation written 2.4 years ago by Brett130
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Answer: A: How can I pick out prokaryotic sequences from a multiple sequence alignment file
... A non sophisticated way of doing it, would be to cut and paste all the accession numbers into the PIR database http://pir.georgetown.edu/pirwww/index.shtml This will bring up all the details for all the sequences. Select from drop down box filters, and select TAXA ID. In this field simply enter 2 ...
written 4.2 years ago by Brett130
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Answer: A: Bioinformatic jobs outside academia?
... There are a number of options open to you. Speaking as a biologist (PhD) working in industry as a Bioinformatican I would recommend marketing yourself as someone that bridges the two disciplines. You recognise the limitations of both biology and IT,  and can translate between the two groups.  This ...
written 4.2 years ago by Brett130
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Answer: A: Protein sequence from EC number and species
... The PIR database is your best bet. http://pir.georgetown.edu/cgi-bin/textsearch.pl You can select function based upon various criteria (eg EC number, GO ID, Kegg Pathway, Enzyme name etc) and you can select organism in a speratre feild  (tax ID, organism name etc). This is probably the most power ...
written 4.5 years ago by Brett130
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Comment: C: Pathway discovery tools (IPA, GENEGO, Pathway studio) for non-pharma analysis ?
... Thanks for brilliant reply Chris.  In an ideal world I would like a program that biologists could use, that’s partly why I have focused upon commercial software. The other half is while I can use free software it usually takes months to get legal approval.   But both those issues though really come ...
written 4.6 years ago by Brett130
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Pathway discovery tools (IPA, GENEGO, Pathway studio) for non-pharma analysis ?
... I am tasked with finding a pathway solution tool for a commercial environment. This is not my area of expertise and I would appreciate any insight you guys could give. I am looking for the best tool to integrate bacterial genomes/data to help discover novel activities and microbial pathways. Within ...
pathway ipa genego pathway studio written 4.6 years ago by Brett130 • updated 4.6 years ago by cdsouthan1.8k
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Homology search beyond standard public databases
... I have an enzyme which is unique in activity and also seemingly extremely rare in nature.  Doing BLAST analysis against standard databases eg NCBI, uniprot yields no results (all <20%). Likewise a crystal structure we have generated yields no structural homologs of any note.  I want to revisit ...
genome homology databases written 4.7 years ago by Brett130 • updated 4.7 years ago by 5heikki8.3k
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Answer: A: Is there anyone who was a pure biologist?
... Any good bioinformatics team, has a range of people with a range of skills. Often you will get pure coders who know nothing about biology, who are greatly assisted by people like you who act as an interface to the real world. Personally I was very much a biologist (in academia), who did bioinformat ...
written 4.9 years ago by Brett130

Latest awards to Brett

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Tools For Fusion-Protein Linker Design
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Gblocks For 16Srna Phylogenetics ?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Pathway discovery tools (IPA, GENEGO, Pathway studio) for non-pharma analysis ?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Bioinformatic jobs outside academia?
Student 4.9 years ago, asked a question with at least 3 up-votes. For Gblocks For 16Srna Phylogenetics ?

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