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PairsDB

http://pairsdb.csc.fi/

Description :
Pairwise alignments of all sequences in UniProt

HOINVGEN

http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html

Description :
INVHOGEN (INVertebrate HOmologous GENes) is a database combining the available invertebrate protein genes from UniProt (consisting of Swiss-Prot, TrEMBL) into gene families. For each family INVHOGEN provides a multiple protein alignment, a maximum likelihood based phylogenetic tree, and taxonomic information about the sequences. It is possible to download the corresponding GenBank flatfiles, the alignment and the tree in Newick format. Sequences and related information have been structured in an ACNUC database under a client/server architecture. Thus, complex selections can be performed. An external graphical tool allows access to the data to evaluate homology relationships between genes and distinguish orthologous from paralogous sequences. INVHOGEN complements the well-known HOVERGEN database.

Aknowledgement :
This work was supported by a grant from the Deutsche Forschungsgemeinschaft (DFG: SFB-TR1). Funding to pay the Open Access publication charges for this article was provided by the Deutsche Forschungsgemeinschaft.

References :
1. Gouy,M., Gautier,C., Attimonelli,M., Lanave,C., di Paola,G. (1985) ACNUC–a portable retrieval system for nucleic acid sequence databases: Logical and physical designs and usage. Comput. Applic. Biosci., 1, 167-172.
2. Duret,L., Perriere,G. and Gouy,M. (1999) HOVERGEN: database and software for comparative analysis of homologous vertebrate genes. In Bioinformatics and Systems, Letovsky, S. (ed.), Kluwer Academic Publishers, Boston, pp. 13-29.

ENDscript

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Description :
ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

PRALINE

http://ibivu.cs.vu.nl/programs/pralinewww/

Description :
Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.

CHC_FIND

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

Description :
CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

ConSeq

http://conseq.bioinfo.tau.ac.il/

Description :
ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue.

Phylogeny.fr

http://www.phylogeny.fr/

Description :
Phylogeny.fr is a seamless automation of the various components in pylogenetic analyses from identification of homologous sequences, construction of multiple alignments, phylogenetic reconstruction to graphical representation of the inferred phylogenetic tree.

MAGNOLIA

http://bioinfo.lifl.fr/magnolia

Description :
MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern.

R-Coffee

http://www.tcoffee.org/

Description :
The R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures.

RNALogo

http://rnalogo.mbc.nctu.edu.tw/

Description :
RNALogo is a tool for graphical representation of features within multiple RNA sequence alignments and their consensus RNA secondary structures. Each RNA family in Rfam has been graphically evaluated for a logo.

PROMALS and PROMALS3D

http://prodata.swmed.edu/promals/promals.php

Description :
PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searchesand secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.

EnteriX

http://globin.cse.psu.edu/enterix/

Description :
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

MAVID

http://baboon.math.berkeley.edu/mavid/

Description :
MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.

MEGA

http://www.megasoftware.net/

Description :
MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments.

MPI Toolkit

http://toolkit.tuebingen.mpg.de/

Description :
Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

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