The bioinformatics tools Kibak commonly uses...
as of Dec07
as of Mar07
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Page Rank as of Mar07 |
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NCBI National Center for Biotechnology Information - I sometimes access this site several times per day... |
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Genomes - The UCSC Genome Browser - now provides access to more than 30 genomes (mostly metazoan). | |||||
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PDB - Protein Data Bank - The principal database of 3D protein structures. |
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AMAP - Multiple Alignment by Sequence Annealing - AMAP is a new approach to multiple sequence alignment that can be accessed from within STRAP. | |||||
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MESHI - Meshi is silk! - MESHI is an opensource collection of Java classes for protein modeling from the Laboratory of Chen Keasar at Ben Gurion University. |
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STRAP 0 - STRuctural Alignment Program for proteins - STRAP is an interactive editor for multiple sequence Alignments. STRAP can also be found here. | |||||
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MyList of useful sites and My University Website |
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CLC Free Work Bench - Free Basic Bioinformatics Package - Linux/2000/XP/Mac versions of the CLC Free Workbench for basic bioinformatics analyses. | |||||
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BioEDIT - Biological Sequence Editor - BioEdit is a sequence alignment editor for 95/98/NT/2000/XP. |
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CMS Resource - Protein Structure Prediction and Modelling - A compendium of tools and resources hosted at the San Diego Supercomputer Consortium. | |||||
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ClustalW ClustalW Nice implementation of this popular multiple alignment program. Outputs postscript trees based on the alignment. |
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ProbCons - Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences - By Chuong Do and Michael Brudno in the Batzoglou Lab. | |||||
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PFP - Patch Finder Plus - Predicts positively charged patches on proteins. From the lab group of Yael Mandel-Gutfreund at the Technion in Haifa. |
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VOROLIGN - Structural Alignment using Voronoi contacts - | |||||
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Primer3 Optimizing Primer Design - Allows you to set a variety of parameters and choose from a set of possible primers. Originally from MIT, now hosted at SourceFourge with many spinoff sites. |
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PrimaClade - Primer design by multiple alignments - | |||||