Protein Similarity

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db... Platforms: *nix

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research. They are licenced under the LGPL. he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction... Platforms: *nix

Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[0] eq $_[1]) ? 1 : -1; } my $matcher = Algorithm::NeedlemanWunsch->new(&score_sub); my $score =... Platforms: *nix

Structure is a screensaver for Mac OS X that draws on the National Center for Biotechnology Information's protein databases to display beautiful 3D protein structures on your screen. It ships with about ten sample structures and via the Internet has seamless access to a database of tens of... Platforms: Mac

The ProtParam widget computes physico-chemical parameters for your protein sequences at ExPASy. You just have to type or paste your sequence in the input field. Platforms: Mac

Come to enjoy our first fractal screensaver. This unique smooth animated fractal dragon will surely impress your imagination. Deep into unlimited self-similarity world of great sets. Blue figure is changing while dragon is running around some points in the complex plain. If it is hard for you to... Platforms: Windows, Windows 8, Windows 7, Windows Server

The FastPCR software was developed to be an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR)... Platforms: Windows, XP, 2003, Windows Vista, XPX64, 7, 7x64

A protein / macromolecule visualization tool that runs as a screensaver module. It colorfully renders PDB (Protein Data Bank) files using unique algorithms. The module automatically annotates, colors, and rotates structures for an educational and captivating display. Show off your research or... Platforms: Mac

A proteomics analyzation software capable of extracting information from the online universal protein resource database UniProt. ProteinID Finder imports your mass spectrometer analyzed protein lists (uniprot accession numbers) into experiments and organizes your proteomics experiments into... Platforms: Mac

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution. Platforms: Windows, Mac, Linux

Several RNA and protein structure volume calculation tools. Platforms: Mac, Linux

The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets. Platforms: Windows, Mac, Linux

BioQuery is a bioinformatics tool that acts as a query builder for genetic, protein, publication, and other biomedical databases. BioQuery is also an update service that periodically resubmits saved searches and sends you new data as it is found. Platforms: Windows, Mac, Linux

Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765 Platforms: Mac, Linux

gbwget is a command line/screen oriented tool to search in nucleotideor protein databases and to view or retrieve database entries. It can easily integrated into the EMBOSS seqence analysis Suite can also be used standalone. Platforms: Windows, Mac, Linux

FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. Platforms: Mac, BSD, Linux

ICRPfinder finds or generates DNA patterns which can include restriction enzyme recognition sites in coding sequences without changing the translated protein sequence. Platforms: Windows, Mac, Linux

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Platforms: Windows, Mac, Linux

This project implements the techniques used in this paper: @INPROCEEDINGS{Andres10a, author = {JesAss Andrés-Ferrer and Germán Sanchis-Trilles and Francisco Casacuberta}, title = {Similarity Word-Sequence Kernels for Sentence Clustering}, booktitle = {Proceedings of the 8th... Platforms: Mac, Linux

JNutrition is a Nutrition Manager. Create meal plans and let it calculate the calories, carbs, protein and fat of it. It is still not finish, but most functions work. Platforms: Mac