web tools for parasite genome projects. parasite functional classification main classes :-...

Web Toolsfor

Parasite GenomeProjects

Parasite Functional Classification Main Classes :-

Metabolism

Energy

Cell Growth, Cell Division & DNA Synthesis

Transcription

Protein Synthesis

Protein Destination

Transport Facilitation

Intracellular Transport

Cellular Biogenesis

Cellular Communication/Signal Transduction

Cell Rescue, Cell Deathand Ageing

Ionic Homeostasis

Hypothetical Proteins

Unclassified Proteins

Steps in production of classification pages :-

1) Awk script produces formatted files of protein annotations.

2) Perl script searches through keyword files for each protein and outputs web pages.

3) Web pages checked for obvious errors/misclassifications and new ‘Unclassifieds’ assigned to classes where appropriate. (Script re-run if necessary.)

4) Users’ feedback (PLEASE!!) taken account of and keyword files modified accordingly.

<TR><TD><small><a href=http://www.ncbi.nlm.nih.gov/htbinpost/Entrez/query?db=p&form=6&uid=7670085&Dopt=g>7670085</a><br><a href=http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=6&uid=AF153838&Dopt=g>AF153838</a><br>AAF66152<br>AF153838<br></small><a href=http://www.ncbi.nlm.nih.gov/blast/blast.cgi?POST&PROGRAM=blastn&DATALIB=nr&INPUT_TYPE=Accession&submit&SEQUENCE=AF153838&EXPECT=10&FILTER=isset&DESCRIPTIONS=50&ALIGNMENTS=50&OVERVIEW=isset>BLASTN</a><br> <a href=http://www.ncbi.nlm.nih.gov/blast/blast.cgi?POST&PROGRAM=blastp&DATALIB=nr&INPUT_TYPE=Accession&submit&SEQUENCE=7670085&EXPECT=10&FILTER=isset&DESCRIPTIONS=50&ALIGNMENTS=50&OVERVIEW=isset>BLASTP</a></TD><TD><small> GLYCEROL KINASE (Leishmania braziliensis) <!-- GLYCEROL KINASE glycerol kinase glycerol kinase --></TD></TR>

Example of formatted sequence annotation :-

decarboxylaseDecarboxylaseDECARBOXYLASElyaseLyaseLYASE

Example keyword file for lyases/decarboxylases :-

Useful Parasite URLs at EBI :-

http://www.ebi.ac.uk/parasites/parasite-genome.html

http://www.ebi.ac.uk/blast2/parasites.html

http://www.ebi.ac.uk/parasites/proteomes.html

http://www.ebi.ac.uk/cgi-bin/parasites/class_search.p

http://www.ebi.ac.uk/cgi-bin/parasites/motif_search.p

http://www.ebi.ac.uk/parasites/leish.html