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Release_To_Do_list

Assigned to: Drexler Hernandez

Contents 1 Background 2 Prodedure 2.1 Getting up to speed 2.2 Getting things in place 2.2.1 Update your current BIRCH to the current Development Version 2.3 Modifying the BLAST menus

Background

The goal is to update the blmenus for the new BLAST+2.2.26 programs from NCBI, that replace the old blastcl3 client.

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program	function	BioLegato menu
blastp	compares protein query to protein database	blprotein --> Database --> blastp
blastx	compares an auto-translated DNA query to a protein database	bldna --> Database --> blastx
blastn	compares a DNA query to a DNA database	bldna --> Database --> blastn
tblastn	compares a protein query to an auto-translated DNA database	blprotein --> Database --> tblastn
tblastx	compares an auto-translated DNA query to an auto-translated DNA database	bldna --> Database --> tblastx
* auto-translation of DNA to protein - Programs like BLAST and FASTA can translate DNA to protein on the fly. This is a very crude translation, involving nothing more than taking every three nucleotides and substituting in the corresponding amino acid. Thus, no information is used regarding introns or transcription initiation or termination sites. Consequently, even non-coding DNA will get translated into protein!

A new blastp blmenu has already been created. Your job is to create blmenus for the remaining four blast programs, in the order shown above.

Prodedure

Getting up to speed

• Tutorial: Use BLASTP to search for sequences related to a query protein, within a specific taxonomic group
• TUTORIAL: CREATING DATASETS OF RELATED SEQUENCES
• NCBI BLAST web site - shows how to run BLAST on the web http://blast.ncbi.nlm.nih.gov/Blast.cgi
• NCBI documentationn for BLAST on the BIRCH web site

Getting things in place

Update your current BIRCH to the current Development Version

Update your copy of BIRCH with both the framework and binaries from the current Development version using the update procedure found in the BIRCH Administrator's Guide

Modifying the BLAST menus

For each program

• create a copy of the blmenu file in $BIRCH/local
• modify the PCD of the blmenu file using guidance from
  • the new blastp menu
  • the NCBI web blast page
  • the manual page for that program

Get blastx working and contact Brian when it's ready. We'll go over the menu and I will make suggestions regarding how to do the remaining programs.