align et align0 calcule un alignement global de deux sequences.
Remarque | Run Unix # align ou align0 | Run Web # |
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The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package.
Remarque | Run Unix # /usr/local/genome/ncbi-blast-2.2.31+/bin/ | Run Web # |
BLAT is a DNA/Protein Sequence Analysis program written by Jim Kent at UCSC. It is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates.
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Cross_Match uses the same algorithm as Swat but also allows the comparison of a pair of sequences to be constrained to bands of the Smith-Waterman matrix that surround one or more matching words in the sequences. This substantially increases speed for large-scale nucleotide sequence comparisons without compromising sensitivity.
Remarque | Run Unix # cross_match | Run Web # |
DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 times faster than BLASTX, finding more than 94% of all matches.
Remarque | Run Unix # diamond COMMAND [OPTIONS] | Run Web # |
A set of sequence comparison tools (fasta36, ggsearch...) used for alignment and database searching.For example, fasta compares a protein sequence to another protein sequence or to a protein database, or a DNA sequence to another DNA sequence or a DNA library.
Remarque | Run Unix # fasta36 | Run Web # |
FSA-BLAST is a new version of the popular BLAST (Basic Local Alignment Search Tool) bioinformatics tool, used to search genomic databases containing either protein or nucleotide sequences. FSA stands for Faster Search Algorithm; FSA-BLAST is twice as fast as NCBI-BLAST with no loss in accuracy.
Remarque | Run Unix # formatdb, cluster, blast, readdb, ssearch | Run Web # |
| Version | MAJ | genewise | | |
| 2.2.0 | 2008-12-10 | Download | Doc |
Genewise permet de comparer une protéine à une banque d'ADN et en prédire sa structure, tout en se déchargeant des problèmes liés au sequencage et d'introns.
Remarque | Run Unix # genewise | Run Web # |
GRAPe is a tool for computing genome re-alignment using marginalized posterior decoding.sTo answer this question, GRAPe uses the Marginalized Posterior Decoding (MPD) algorithm which uses the posterior distribution of alignments to optimize the correct assignment of homology of individual nucleotides, instead of finding a single most probable alignment. Simulations show that the MPD algorithm has higher sensitivity and specificity than the Viterbi and Needleman-Wunsch algorithms.
Remarque | Run Unix # grape | Run Web # |
| Version | MAJ | Klast | | |
| 4.4 | 2015-04-24 | Download | Doc |
KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.
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PLAST : Parallel Local Alignment Search Tool
Remarque | Run Unix # plastall | Run Web # |
SIM4 recherche les meilleurs alignements locaux entre une séquence d'ADNc et une séquence d'ADN génomique (ARNm, EST) contenant ce gène et autorisant la présence d'introns et un petit nombre d'erreurs de séquençage.
Remarque http://globin.cse.psu.edu/html/docs/sim4.html| Run Unix # sim4 mouse_cDNA human_genomic K=15 C=11 A=3 W=10 | Run Web # |
| Version | MAJ | swat | | |
| | Download | Doc |
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Washington University BLAST (WU BLAST) version 2.0 is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases.
Remarque | Run Unix # wu-blastall | Run Web # |
YASS est un outil permettant la recherche locale de similaritées dans les séquences d'ADN.
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