Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Alignement de paires


VersionMAJ

align

2.0u2003-11-28DownloadDoc
align et align0 calcule un alignement global de deux sequences.

Remarque
Run Unix # align ou align0Run Web #

VersionMAJ

blast

2.2.262012-03-07DownloadDoc

Remarque
Run Unix # blastallRun Web # https://migale.jouy.inra.fr/?q=blast

VersionMAJ

blast+

2.2.312015-08-24DownloadDoc
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 #

VersionMAJ

blat

342008-01-11DownloadDoc
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.

Remarque
Run Unix # blatRun Web #

VersionMAJ

cross_match

0.9903292002-11-06DownloadDoc
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_matchRun Web #

VersionMAJ

diamond

0.7.92015-12-02DownloadDoc
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 #

VersionMAJ

fasta

3.62014-02-21DownloadDoc
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 # fasta36Run Web #

VersionMAJ

FSA-BLAST

1.032005-12-16DownloadDoc
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, ssearchRun Web #

VersionMAJ

genewise

2.2.02008-12-10DownloadDoc
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 # genewiseRun Web #

VersionMAJ

grape

1.12008-10-21DownloadDoc
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 # grapeRun Web #

VersionMAJ

Klast

4.42015-04-24DownloadDoc
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.

Remarque
Run Unix # Run Web #

VersionMAJ

plast

1.02009-06-08DownloadDoc
PLAST : Parallel Local Alignment Search Tool

Remarque
Run Unix # plastallRun Web #

VersionMAJ

sim4

2003-09-212006-03-28DownloadDoc
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=10Run Web #

VersionMAJ

swat

DownloadDoc

Remarque
Run Unix # Run Web #

VersionMAJ

wu-blast

2.02005-02-14DownloadDoc
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-blastallRun Web #

VersionMAJ

yass

1.142010-03-16DownloadDoc
YASS est un outil permettant la recherche locale de similaritées dans les séquences d'ADN.

Remarque
Run Unix # yassRun Web #

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