Sequence analysis

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==Software==
==Software==
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* [[ARB]] - Microbiologist's sequence database tool
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* [[ARB]] Microbiologist's sequence database tool
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* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
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* [[BioJava]] The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
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* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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* [[Biopython]] The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
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* [[BioWish]] Biowish is a C-extension for the Tcl/Tk scripting language
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* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
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* [[BLAST]] (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
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* [[clustalw]] - The famous ClustalW multiple alignment program  
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* [[clustalw]] The famous ClustalW multiple alignment program  
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* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program  
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* [[clustalx]] Clustal X provides a window-based user interface to the ClustalW multiple alignment program  
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* [[DNA-GUI]] - DNA Graphical User Interface
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* [[COTRASIF]] — a free tool for genome-wide detection of putative TFBS in the promoters of the eukaryotic genes.
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* [[EMBOSS]] - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
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* [[DNA-GUI]] DNA Graphical User Interface
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* [[MPSRCH]] - MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
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* [[EMBOSS]] EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
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* [[NCRNASCAN]] - a structural RNA genefinder
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* [[MPSRCH]] MPSRCH™ is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
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* [[PatScan]] - PatScan is a  pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
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* [[NCRNASCAN]] a structural RNA genefinder
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* [[PKNOTS]] - RNA pseudoknot prediction
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* [[PatScan]] PatScan is a  pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
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* [[Pratt]] - a pattern discovery tool
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* [[PKNOTS]] RNA pseudoknot prediction
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* [[readseq]] - Reads and writes nucleic/protein sequences in various format  
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* [[Pratt]] a pattern discovery tool
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* [[SEALS]] - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
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* [[readseq]] Reads and writes nucleic/protein sequences in various format  
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* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
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* [[SEALS]] SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
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* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
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* [[sp2fasta]] produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
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* [[tRNAscan-SE]] - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
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* [[Toucan]] A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
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* [[WU-Blast]] - Washington U. [[BLAST]]
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* [[tRNAscan-SE]] tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
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* [[WU-Blast]] Washington U. [[BLAST]]
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* [[UGENE]] — a free and open source DNA and protein sequence analysis tool. The goal of the project is to integrate most of the available command line utilities into a single graphical package.

Revision as of 15:46, 18 February 2010

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