Login or Register to Ask a Question and Join Our Community


Software Releases - RSS News

Basic Local Alignment Search Tool 2.2.19 (Default branch)

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Special Forums News, Links, Events and Announcements Software Releases - RSS News Basic Local Alignment Search Tool 2.2.19 (Default branch)
# 1  
Old 12-18-2008
Basic Local Alignment Search Tool 2.2.19 (Default branch)
BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity. It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems. License: Open Software License Changes:
The BLASTDB environment variable now supports multiple database search paths. When possible, a smaller protein lookup table is used to improve performance. formatrpsdb now supports creating databases larger than 2G. seedtop now supports searches with gi lists. The X3 value for blastn/megablast was corrected. Image

Image

More...
Login or Register to Ask a Question

Previous Thread | Next Thread

2 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Alignment tool to join text files in 2 directories to create a parallel corpus

I have two directories called English and Hindi. Each directory contains the same number of files with the only difference being that in the case of the English Directory the tag is .english and in the Hindi one the tag is .Hindi The file may contain either a single text or more than one text... (7 Replies)
Discussion started by: gimley
7 Replies

2. Shell Programming and Scripting

Help needed with basic search

hi, im trying to find the longest word in /usr/share/dict/words that does not contain the letter i. i've tried using the wc -L command like so: $ wc -L /usr/share/dict/words which basically tells me the longest word which is good but how do i get the longest word which Does not contain the... (7 Replies)
Discussion started by: tryintolearn
7 Replies
Login or Register to Ask a Question

LEARN ABOUT DEBIAN

bp_search2tribe

BP_SEARCH2TRIBE(1p)					User Contributed Perl Documentation				       BP_SEARCH2TRIBE(1p)

NAME

       search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

SYNOPSIS

       Usage:
	 search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

DESCRIPTION

       This script is probably too slow for most people's uses.  It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output
       from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL
       with the mcxdeblast script and the --m9 option.

       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.

       The options are:

	  -o filename	       - the output filename [default STDOUT]
	  -f format	       - search result format (blast, fasta)
				 (ssearch is fasta format). default is blast.
	  -w or --weight VALUE - Change the default weight for E(0.0) hits
				 to VALUE (default=200 (i.e. 1e-200) )
	  -h		       - this help menu

       Additionally specify the filenames you want to process on the command-line.  If no files are specified then STDIN input is assumed.  You
       specify this by doing: search2tribe < file1 file2 file3

AUTHOR

       Jason Stajich, jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02						       BP_SEARCH2TRIBE(1p)