核酸序列分析

★Analysis and Annotation Tool for Finding Genes in Genomic Sequences
5-3-2-DcDPDFWE/USA
http://genome.cs.mtu.edu/aat.html
Identifies genes in a DNA sequence by comparing it to cDNA and protein sequence databases (including those at HGI, TIGR, dbEST, Swiss-Prot and nr).

★Pairwise Sequence Alignment
3-4-2-DcUPUFWE/USA
http://genome.cs.mtu.edu/align/align.html
Computes the global alignment between two sequences. Compare DNA with DNA, cDNA or protein. For DNA and cDNA, settings (gap open penalty, gap extension etc.) can be defined.


★Multiple Sequence Alignemnt with MAP
4-3-2-DcUPUFWE/USA
http://genome.cs.mtu.edu/map/map.html
Calculates the global alignment of DNA or protein sequences using an algorithm which computes the best overlapping alignment without penalising terminal gaps. Long internal gaps in short sequences are not penalised.

★Network Protein Sequence Analysis
5-4-1-PUW/France
http://pbil.ibcp.fr/NPSA/npsa_clustalw.html
ClustalW multiple sequence alignment.

★ALIGN
5-1-1-DUPUWE/France
http://www2.igh.cnrs.fr/bin/align-guess.cgi or http://genome.eerie.fr/fasta/align-query.html
Applies the BLOSUM50 matrix to deduce the optimal alignment between two sequences.

★Multiple Sequence Alignment with Hierarchial Clustering
5-5-3-PUW/France
http://www.toulouse.inra.fr/multalin.html
Sequence alignment with a colour output where differing or similar amino acids in the alignment can be highlighted.

★Colour INteractive Editor for Multiple Alignments (CINEMA)
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/default.htm
A comprehensive and popular site. Allows the user to visualise and manipulate aligned protein sequences.
Makes use of Java. I recommend you access this site from a fast workstation!

★VSNS BioComputing Division Multiple Alignment Resource Page
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/default.htm
An excellent, comprehensive resource for multiple sequence alignment, software and tutorials.