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JAligner
38415
JAligner
http://jaligner.sourceforge.net/
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
Biology > Bioinformatics > Online Services > Protein Analysis
jaligner pairwise local java sequence alignment affine gap open source smith-waterman algorithm
Jan 6, 2008
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Other links at Biology > Bioinformatics > Online Services > Protein Analysis
1. UniProt
UniProt (Universal Protein Resource) is a comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
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2. COLORADO3D
Service to aid visualisation of potential errors in protein structures. Free for academic users.
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Calculated using the FASTA amino acid sequence and pKa values for. Allows consideration of post-translational modifications.
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4. Swiss-Model
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
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An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design.
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6. Dali server
The Dali server is a network service for comparing protein structures in 3D.
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The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, a computer-annotated supplement, which contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database, which are not yet integrated into SWISS-PROT.
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User-friendly interface allowing analysis of several proteins at once, including superimposition to deduce structural alignments, and compare active sites. From GlaxoWellcome Experimental Research, Geneva, Switzerland.
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9. ProtFun
Ab initio predictions of protein function from protein sequence. The method works by integrating various predicted post-translational and localizational aspects of the proteins submitted.
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Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast.
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