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vit-embnet.unil.ch

EMBnet node Switzerland

Bioinformatics tools, databases. Pretty printing of MSAs. MSA (Multiple Sequence Alignment). Comparison with coiled-coils database. Obtain sequence from database. Access to tools and DBs. Extract DNA segments between two primers. Alignment of 2 sequences. Optimal score of alignment. More resources: ExPASy: SIB Bioinformatics Resources Portal. Education, courses, documentation. SIB bioinformatics course portal. EMBnet course list archive. MD tutorial.tar.gz. BLAST - replacement: BLAST on ExPASy.

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EMBnet node Switzerland | vit-embnet.unil.ch Reviews
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Bioinformatics tools, databases. Pretty printing of MSAs. MSA (Multiple Sequence Alignment). Comparison with coiled-coils database. Obtain sequence from database. Access to tools and DBs. Extract DNA segments between two primers. Alignment of 2 sequences. Optimal score of alignment. More resources: ExPASy: SIB Bioinformatics Resources Portal. Education, courses, documentation. SIB bioinformatics course portal. EMBnet course list archive. MD tutorial.tar.gz. BLAST - replacement: BLAST on ExPASy.
<META>
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1 embnet node switzerland
2 boxshade
3 clustalw
4 coils
5 fetch
6 ftp server
7 ipcr
8 lalign
9 prss
10 tmpred
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EMBnet node Switzerland | vit-embnet.unil.ch Reviews

https://vit-embnet.unil.ch

Bioinformatics tools, databases. Pretty printing of MSAs. MSA (Multiple Sequence Alignment). Comparison with coiled-coils database. Obtain sequence from database. Access to tools and DBs. Extract DNA segments between two primers. Alignment of 2 sequences. Optimal score of alignment. More resources: ExPASy: SIB Bioinformatics Resources Portal. Education, courses, documentation. SIB bioinformatics course portal. EMBnet course list archive. MD tutorial.tar.gz. BLAST - replacement: BLAST on ExPASy.

INTERNAL PAGES

vit-embnet.unil.ch vit-embnet.unil.ch
1

Guides

http://vit-embnet.unil.ch/pages/docs-guides.html

A Quick Guide to PERL. Download pdf file (0.7 Mb). A Quick Guide to PERL Regular Expressions. Download pdf file (0.7 Mb ). A Quick Guide to BLAST. Download pdf file (1.7 Mb). A Quick Guide to wEMBOSS. Download pdf file (2.7 Mb ). A Quick Guide to Phrap. Download pdf file (1.7 Mb ). A Quick Guide to Phred. Download pdf file (1.7 Mb ). A Quick Guide to ExPASy. Download pdf file (1.7 Mb). A Quick Guide to SWISS-MODEL. Download pdf file (1.7 Mb ). A Quick Guide to EMBOSS. Download pdf file (1.7 Mb ).

2

TMpred Server

http://vit-embnet.unil.ch/software/TMPRED_form.html

Prediction of Transmembrane Regions and Orientation. The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring. K Hofmann and W. Stoffel. TMbase - A database of membrane spanning proteins segments. Biol Chem. Hoppe-Seyler 374. For further information see the TMbase.

3

PRSS Server

http://vit-embnet.unil.ch/software/PRSS_form.html

PRSS3 - evaluates the significance of a protein sequence alignment. Prss3 also allows a more sophisticated shuffling method: residues can be shuffled within a local window, so that the order of residues 1-10, 11-20, etc, is destroyed but a residue in the first 10 is never swapped with a residue outside the first ten, and so on for each local window. This program is part of the FASTA package of sequence analysis program. Paste your two sequences in one of the supported formats. Number of shuffles :.

4

Fetch Server

http://vit-embnet.unil.ch/software/fetch.html

ID or AC :. SIB Swiss Institute of Bioinformatics. Back to the Top.

5

COILS Server

http://vit-embnet.unil.ch/software/COILS_form.html

Prediction of Coiled Coil Regions in Proteins. COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. COILS was described in:. Lupas, A., Van Dyke, M., and Stock, J. (1991). Predicting Coiled Coils from Protein Sequences,. Back to the Top.

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EMBnet node Switzerland

Bioinformatics tools, databases. Pretty printing of MSAs. MSA (Multiple Sequence Alignment). Comparison with coiled-coils database. Obtain sequence from database. Access to tools and DBs. Extract DNA segments between two primers. Alignment of 2 sequences. Optimal score of alignment. More resources: ExPASy: SIB Bioinformatics Resources Portal. Education, courses, documentation. SIB bioinformatics course portal. EMBnet course list archive. MD tutorial.tar.gz. BLAST - replacement: BLAST on ExPASy.

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