Free basic local alignment search tool software for linux

Basic Local Alignment Search Tool 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.
Main features:
Nucleotide
- Quickly search for highly similar sequences (megablast)
- Quickly search for divergent sequences (discontiguous megablast)
- Nucleotide-nucleotide BLAST (blastn)
- Search for short, nearly exact matches
- Search trace archives with megablast or discontiguous megablast
Protein
- Protein-protein BLAST (blastp)
- Position-specific iterated and pattern-hit initiated BLAST (PSI- and PHI-BLAST)
- Search for short, nearly exact matches
- Search the conserved domain database (rpsblast)
- Protein homology by domain architecture (cdart)
Translated
- Translated query vs. protein database (blastx)
- Protein query vs. translated database (tblastn)
- Translated query vs. translated database (tblastx)
Genomes
- Human, mouse, rat, chimp cow, pig, dog, sheep, cat
- Chicken, puffer fish, zebrafish
- Environmental samples
- Protozoa
- Insects, nematodes, plants, fungi, microbial genomes, other eukaryotic genomes
Special
- Search for gene expression data (GEO BLAST)
- Align two sequences (bl2seq)
- Screen for vector contamination (VecScreen)
- Immunoglobin BLAST (IgBlast)
- SNP BLAST
Meta
- Retrieve results

Amazon API Search is the beginnings of a perl script to search Amazon.

It interfaces with Amazons API interface and performs whatever search the user desires, it then parses the data returned and inserts it in to an MySQL table.

Currently the script only deals with basic returned data, and does not have a user interface. In future releases I hope to correct this.

The script is certainly worth a look for anyone interested in using Amazons API interface.

Javascript Search Aggregator allows you to perform all of your Web searches from one place.
You can create many categories of searches such as work and fun and customize search engines for your specific needs.
Javascript Search Aggregator remembers the last query and state of the tabs and works on any browser with JavaScript support.
Enhancements:
- Do not load last selected engine on first load

Bio::Graphics::Glyph::alignment is the "alignment" glyph.

SYNOPSIS

See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >.

This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is proportionate to the score.

Bio::Tools::AlignFactory is a base object for alignment factories.

SYNOPSIS

You wont be using this as an object, but using a dervied class like Bio::Tools::pSW

Holds common Alignment Factory attributes in place

nautilus-search-tool is a Nautilus extension to have "search files" on popup menu.

Search::Tools are tools for building search applications.

SYNOPSIS

use Search::Tools;

my $re = Search::Tools->regexp(query => the quick brown fox);

my $snipper = Search::Tools->snipper(query => $re);

my $hiliter = Search::Tools->hiliter(query => $re);

for my $result (@search_results)
{
print $hiliter->light( $snipper->snip( $result->summary ) );
}

Search::Tools is a set of utilities for building search applications. Rather than adhering to a particular search application, the goal of Search::Tools is to provide general-purpose methods for common search application features. Think of Search::Tools like a toolbox rather than a hammer.

Examples include:

Parsing search queries for the meaningful keywords
Rich regular expressions for locating keywords in the original indexed documents
Contextual snippets showing query keywords
Highlighting of keywords in context

Search::Tools is derived from some of the features in HTML::HiLiter and SWISH::HiLiter, but has been re-written with an eye to accomodating more general purpose features.