Sequence Analysis wwwTools
Rein's compact collection of www-links for DNA and protein sequence analysis.
almost all you need
[Last updated 28-July-2007]

Database Searches DNA Tools Protein Tools
SRS-EMBL General Sequence database query Translate a DNA sequence at ExPASy, at EBI or at the Virtual Genome Center Predict secondary structure with Burkhard Rost's PHD - now in New York! or David Jones' PSIpred.
SRS5-Oslo General Sequence database query (unavailable) Pairwise BLAST at NCBI Use Inge Jonassen's web PRATT to find patterns in a set of protein sequences.
SRS6-EBI General Sequence database query Pairwise alignment at BCM Predict Transmembrane regions and coiled-coil regions at ISREC/EMBnet-CH
Querey Pfam domain database

Restriction enzymes: R.Robert's REBASE and Restriction enzyme cutting with Pierre Rodrigues' SeqCutter.

Pairwise Blast of protein sequences;
[change program to Blastp]
BLAST: Database searches

Self-Dotplots at the Virtual Genome Center

Pairwise alignment at ExPASy
BCM: Database searches, patterns. Sequence conversion with Don Gilbert's ReadSeq at BIMASS. Protein Parameters, aa-composition, mw, pI etc. at ExPASy
Scan your sequence for Prosite patterns with ScanProsite at ExPASy Multiple Sequece Alignments, ClustalW, PIMA etc. at BCM.
But use rather Clustal_X
including a HMM-based protein domain searching system by Sean Eddy et al. Washington U., St. Louis.
PRINTS Protein Motif Database at U. College London PCR primer selection at U. Minnesota Random sequence generator at ExPASy.
ENTREZ: Nucleotide sequence database query at NCBI Estimation of Tm for an oligo at U. Minnesota. Generate a 3D-model of your protein using Swiss-Model at ExPASy.
ENTREZ: Protein sequence database query at NCBI GRAIL gene prediction at ORNL www-BoxShade, decoration of multiple alignments at the Swiss EMBnet node
BLAST unfinished human genome Sequence utilities at BCM, including primer selection, reverse complement, restriction sites, translation, identification of repetitive sequences. PDB - Protein structure databank and RasMol for viewing.
BLAST unfinished microbial genomes. CINEMA: Multiple sequence editor from T.K.Attwood. PSORT - Prediction of protein sorting signals, including nuclear localisation signals at IMCB, Osaka University.
Wonder what happened to the NLS-predictor at Cambridge
INTERPRO - integrated protein domain database. Protein Machine at EBI Multiple Sequece Alignments, ClustalW, PIMA etc. at BCM

Credits to all those who spend time and efforts providing all these friendly tools.
This list is NOT meant to be exhaustive. If you are looking for other tools and www-services, take a look at:

ExPASy's Tool Chest or
Pedro's Collection of BioMolecular Research Tools
A collection of links related to the analysis of Phylogeny
Yuerong Zhu's list and
the one from IMB at the Austrian Academy of Sciences
are also pretty comprehensive.
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This page was created by Rein Aasland, July 22. 1996.