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• Instructions to users
• Bioinformatics Wiki
• Intelligent Interface to Sequence Analysis
• July - August 2006

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IISA 1.0 (21 July 2006)

This is just a test release. The release contains 3 files.

1. IISA.pm is the perl module file.
2. Protein.pl – The first perl script which retrieves the sequence and submits to protparam at expasy. It parses the page returned by protparam and writes the data as a prolog file (protparam_output.pro).
3. Protparam.pro – The prolog file which loads the previous files and adds the rules.

IISA 2.0 (23 July 2006)

The files were renamed as below.

• protein.pl is renamed protparam.pl. It will submit the sequence to protparam @ expasy and parse the results. The output prolog file is protparam_output.pro. Format: factor(value).

• phosp.pl is added. It will find the phosphorylation sites in the protein and write the output to phosphorylation.pro. Format: phosphorylation_site(phosphorylated aminoacid, position, pattern, score).

• proscan.pl is added. It will find the prosite patterns in the sequence. The output file is proscan_output.pro. Format: proscan(name of motif, begin, end, pattern).

• protparam.pro changed to protein.pro, the main prolog file which consults the output files and adds rules.

• Readme.rtf

IISA 3.0 (26 July 2006)

• coil.pl added. It will find the coiled coil areas. Format: coil(position, residue, probability).

IISA 3.1 (04 August 2006)

• BLASTP.PL

Description: Finds similar proteins by doing a blast search on SWISSPROT through NPSA server.

Output: blastp_output.pro

Format: blastp(swissprotid, sequenceid, sequence_name, e-score).

IISA 3.2 (07 August 2006)

• PHDHTM.PL

Description: TRANSMEMBRANE HELICES PREDICTION @ NPSA

Output: phdhtm_output.pro

Format: transmembrane_helix_length(length).

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