The ISREC Software Homepage

This page contains a small collection of remotely-executable software. All of them use the WWW-forms interface and require a WWW-browser with forms capabilities (like Mosaic 2.0 and higher).

Servers maintained by the ISREC bioinformatics group:

ProfileScan

(Search a the profiles-entries in PROSITE with your sequence). This is an experimental implementation of the pfscan program. The profile-entries contained in PROSITE, recognizable by the keyword MATRIX, can be searched with a single, user-supplied sequence.

Frame-ProfileScan

(Search a the profiles-entries in PROSITE with a DNA sequence). This is new experimental service performs a frame-tolerant ProfileScan of a short DNA sequence against a collection of protein profiles.

PrositeScan

(Search the PROSITE database with your sequence). This is a PERL-implementation of a program searching the current release of the PROSITE database using regular expressions.

PatternFind

(Search a protein database with a pattern). This PERL-Program takes a user-defined pattern (PROSITE-format or regular expression) and searches a protein database. It offers several useful output options.

SAPS

(Statistical Analysis of Protein Sequences). This program, written by the group of Samuel Karlin, analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc. One of its options is to generate self-explanatory output.

Dotlet

(A Java applet for sequence comparisons using the dot matrix method).

Hits

(A database devoted to protein domains). It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them.

Servers maintained by the Swiss EMBNet node:

ESTScan

(Gene prediction for EST sequences). This program detects and reconstructs coding regions from EST sequences applying an automatic frameshift error correction mechanisms.

NCBI-BLAST

(Fast sequence similarity search). This form runs NCBI BLAST2 on our local server at ISREC in Lausanne. The databases are updated weekly.

WU-BLAST

(Fast sequence similarity search). This form runs WU-BLAST on our local server at ISREC in Lausanne. The databases are updated weekly. WU-BLAST is recommended for searches where the goal is to find moderate to weak similarities between non-coding nucleic acid sequences.

TMpred

(Prediction of transmembrane regions). This program tries to find putative transmembrane domains in proteins and also speculates on the possible orientation of these segments. For its scoring, it uses a combination of multiple weight-matrices that have been extracted from a statistical analysis of TMbase, a collection of all annotated transmembrane proteins present in SwissProt.

Coils

(Prediction of coiled coil regions). This program predicts (2 stranded) coiled coil regions in proteins by the Lupas-algorithm.

BOXSHADE 3.21

(pretty printing of multiple alignments). This program generates publication-quality (or editable) graphics from multiple-alignment files. Many different input- and output-formats are supported. Conserved and/or similar residues are emphasized by various degrees of shading. It is also possible to specify a similarity-threshold that has to be reached for shading a residue.

To get information on our profile-related programs and to access our experimental profile-search server, you should go to the profile page.

Go to the ISREC-bioinformatics home page