Basic Local Alignment Search Tool 2.2.19 (Default branch)


 
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
Class::DBI::Search::Basic(3pm)				User Contributed Perl Documentation			    Class::DBI::Search::Basic(3pm)

NAME
Class::DBI::Search::Basic - Simple Class::DBI search SYNOPSIS
my $searcher = Class::DBI::Search::Basic->new( $cdbi_class, @search_args ); my @results = $searcher->run_search; # Over in your Class::DBI subclass: __PACKAGE__->add_searcher( search => "Class::DBI::Search::Basic", isearch => "Class::DBI::Search::Plugin::CaseInsensitive", ); DESCRIPTION
This is the start of a pluggable Search infrastructure for Class::DBI. At the minute Class::DBI::Search::Basic doubles up as both the default search within Class::DBI as well as the search base class. We will probably need to tease this apart more later and create an abstract base class for search plugins. METHODS
new my $searcher = Class::DBI::Search::Basic->new( $cdbi_class, @search_args ); A Searcher is created with the class to which the results will belong, and the arguments passed to the search call by the user. opt if (my $order = $self->opt('order_by')) { ... } The arguments passed to search may contain an options hash. This will return the value of a given option. run_search my @results = $searcher->run_search; my $iterator = $searcher->run_search; Actually run the search. SUBCLASSING
sql / bind / fragment The actual mechanics of generating the SQL and executing it split up into a variety of methods for you to override. run_search() is implemented as: return $cdbi->sth_to_objects($self->sql, $self->bind); Where sql() is $cdbi->sql_Retrieve($self->fragment); There are also a variety of private methods underneath this that could be overridden in a pinch, but if you need to do this I'd rather you let me know so that I can make them public, or at least so that I don't remove them from under your feet. perl v5.12.4 2011-08-10 Class::DBI::Search::Basic(3pm)