Bioinformatics Tools

Esta página es de solo lectura. Puedes ver la fuente pero no puedes cambiarla. Pregunta a tu administrador si crees que esto es incorrecto.
==== Pairwise Alignments ====

[[http://www.ebi.ac.uk/Tools/psa/emboss_needle/ | Needle: Pairwise Alignment Algorithms:]] you can obtein **Identity** and **Similarity**

[[http://blast.genome.ad.jp/ | BLAST (Japan):]] you can do direct clustalW analysis

[[http://www.ebi.ac.uk/Tools/emboss/align/ | EMBOSS Pairwise Alignment Algorithms:]] you can obtein **Identity** and **Similarity**

[[http://blast.ncbi.nlm.nih.gov/Blast.cgi|BLAST (NCBI):]] Basic Local Alignment Search Tool. finds regions of similarity between biological sequences

[[http://www.soe.ucsc.edu/research/compbio/sam.html|SAM]]: UCSC's Sequence Alignment and Modeling System

[[http://expasy.org/tools/sim-prot.html | SIM]]: Alignment Tool for protein sequences


[[http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi |ESPRIPT:]] Easy Sequencing in PostScript: alignment and secondary structure scheme for publications. [###TOP##]

==== Multiple Alignments ====

[[http://tcoffee.crg.cat | Tcoffe]]: A Program for Multiple Sequence Alignment

[[http://www.ebi.ac.uk/Tools/msa/clustalo/ | clustalO:]]Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments

[[http://www.ebi.ac.uk/Tools/msa/|EMBL-EBI:]]Multiple Sequence Alignment (MSA)

[[http://barton.ebi.ac.uk/servers/amas_server.html | AMAS Server:]] Analyse Multiply Aligned Sequences

[[http://www.compbio.dundee.ac.uk/software.html#msa | Barton lab:]]Multiple Sequence Alignment and Analysis

[[http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi |## ESPRIPT:]] Easy Sequencing in PostScript: alignment and secondary structure scheme for publications

==== Structural Alignments ====

[[http://webapps.embl-hamburg.de/rapido/ | RAPIDO]] is an algorithm for the 3D alignment of protein structures. In order to align your protein structures:output =RMSD. you can upload multiples PDB files (tarball.tgz <list-of-pdb-files>).

[[http://raptorx.uchicago.edu/ |RaptorX]] Structure Alignment - protein pairwise and/or multiple structure alignment

[[http://www.bioinformatics.org/strap/ | Strap:]] intuitive Editor for annotated multiple Sequence and Structure Alignments

[[http://zhanglab.ccmb.med.umich.edu/TM-align/ | TM-align:]] A protein structure alignment algorithm using TM-score rotation matrix

[[http://cssb.biology.gatech.edu/skolnick/webservice/TM-align/index.shtml | TM-align]]

[[http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html | Online]] Structure Alignment Resources (list)

[[http://www.ebi.ac.uk/Tools/dalilite/index.html | pairwise DaliLite server]]: superimpose two particular structures

[[http://www.tcoffee.org/Projects_home_page/trmsd.html | T-RMSD]] (Tree based on Root Mean Square Deviation): is a distance RMSD (dRMSD) based method which generate Structural Trees (analogue to phylogenetic tree) to determine fine-grained structural variations associated with a given Multiple Sequence Alignment. It is part of the T-Coffee distribution. 

[[http://www.compbio.dundee.ac.uk/Software/Stamp/stamp.html | Stamp:]] STAMP is a suite of programs for the comparison and alignment of protein three dimensional structures.

[[http://www.cathdb.info/cgi-bin/SsapServer.pl| SSAP:]] The SSAP server allows users to compare the structures of two proteins and view the subsequent structural alignment

==== Softwares ====


[[http://www.drive5.com/muscle/download3.6.html | MUSCLE:]]protein multiple sequence alignment software

[[ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ | ClustalW]]

[[http://align.bmr.kyushu-u.ac.jp/mafft/software/ | MAFFT ver.5]] - a multiple sequence alignment program

[[http://journals.iucr.org/sincris-top/logiciel/prg-stamp.html | SINCRIS software, Stamp:]] structural alignment

[[http://asap.ahabs.wisc.edu/mauve/index.php | Mauve]] is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.


==== alignment editors/ viewer ====

[[http://pfaat.sourceforge.net/ | PFAAT:]]Protein Family Alignment Annotation Tool

[[http://www.jalview.org/download.html | JalView]]

[[http://align.bmr.kyushu-u.ac.jp/xced/ | XCED]] - a multiple sequence alignment editor

[[http://www.charite.de/bioinf/strap/ | multiple sequence alignment]]: Interactive Editor STRAP

[[http://www.mbio.ncsu.edu/BioEdit/BioEdit.html |BioEdit]] is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.  

[[http://pbil.univ-lyon1.fr/software/seaview.html | SeaView]] is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment.

[[http://www.cs.ubc.ca/~tmm/papers/sj/ | SequenceJuxtaposer:]] Fluid Navigation For Large-Scale Sequence Comparison In Context

[[http://espript.ibcp.fr/ESPript/ESPript/ | ESPript]], Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences

==== others tools ====


[[http://www.geneious.com | Geneious Pro:]] is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc.

[[http://wavis.img.cas.cz/ | Alignment visualization tools server:]] These tools should help you with preparation of publication-quality pictures of your alignment. Description ot the server and examples of its use are in the help page.

[[http://weblogo.berkeley.edu/ | WebLogo]] is a web based application designed to make the generation of sequence logos as easy and painless as possible

[[http://moraine.cebitec.uni-bielefeld.de/ | MoRAine]] is a tool for the reannotation of transcription factor binding motifs and the creation of sequence logos
Bioinformatics Tools

Herramientas de usuario

Herramientas del sitio

Herramientas de la página
