Free alignment search 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

Archive Search is an extension which displays an archived versions of the webpage.

Displays an archived versions of the webpage.

First click: Internet Archive
Second click: Google cache
Third click: Yahoo
Fourth click: MSN

Answers.com Search is a Superkaramba theme that searches Answers.com.

If you tried this theme before and it doesnt works for you, please try this new version since it fixes a major problem that used to prevent the theme from working.

DGS Search was created to provide an easy to install search utility capable of handling filesystem and database searches on UNIX and Windows based platforms.

DGS Search is aimed at supporting the small to medium sized web site.

City info search enables you to get all the information about any city in the USA with a mouse click.

Get all the information about any city in the USA with a mouse click. This includes geography, population, ethnic composition, housing, climate, hospitals, airports, etc.

Usage: highlight the name on any US city on a page. Right click the mouse. Choose Get City Info.

No annoing toolbars.

Web search is provided with Yahoo! Search Web Services. Okapibar consists of a keyword input, search engine buttons, and function buttons. The search engine button selects YahooCPM or Yahoo. The function buttons are a highlight button to change the background color of words same as the key words, a compact button to change between one line and two-line layout, and a script button to show that Javascript is disable during the search in CPM.

Net::Google::Search is a simple OOP-ish interface to the Google SOAP API for searching.

SYNOPSIS

use Net::Google::Search;
my $search = Net::Google::Search->new(%args);

$search->query(qw(aaron cope));
map { print $_->title()."n"; } @{$search->results()};

# or

foreach my $r (@{$search->response()}) {
print "Search time :".$r->searchTime()."n";

# returns an array ref of Result objects
# the same as the $search->results() method
map { print $_->URL()."n"; } @{$r->resultElement()}
}

Provides a simple OOP-ish interface to the Google SOAP API for searching.
This package is used by Net::Google.

Cook County PIN Search provides a title search tool.

Cook County (IL, USA) Property Index Number Search

A title search tool. If in the course of your browsing you come across a Cook County Property Index Number (PIN) (format 99-99-999-999 or 99-99-999-999-9999) in your browser window, select it and "right"-click and on the context menu you will be offered options to open new tabs of relevant information from Cook County websites.