Sequence analysis

From Bioinformatics.Org Wiki

Software

• ARB - Microbiologist's sequence database tool
• BioJava - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
• Biopython - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
• BioWish - Biowish is a C-extension for the Tcl/Tk scripting language
• BLAST - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
• clustalw - The famous ClustalW multiple alignment program
• clustalx - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
• DNA-GUI - DNA Graphical User Interface
• EMBOSS - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
• MPSRCH - MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
• NCRNASCAN - a structural RNA genefinder
• 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
• PKNOTS - RNA pseudoknot prediction
• Pratt - a pattern discovery tool
• readseq - Reads and writes nucleic/protein sequences in various format
• SEALS - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
• sp2fasta - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
• Toucan - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
• 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.
• WU-Blast - Washington U. BLAST
• 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.