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Web Tools for Parasite Genome Projects

Web Tools for Parasite Genome Projects. Parasite Functional Classification Main Classes :-. Metabolism Energy Cell Growth, Cell Division & DNA Synthesis Transcription Protein Synthesis Protein Destination Transport Facilitation. Intracellular Transport Cellular Biogenesis

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Web Tools for Parasite Genome Projects

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  1. Web Tools for Parasite Genome Projects

  2. 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 Death and Ageing Ionic Homeostasis Hypothetical Proteins Unclassified Proteins

  3. 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.

  4. Example of formatted sequence annotation :- <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>

  5. Example keyword file for lyases/decarboxylases :- decarboxylase Decarboxylase DECARBOXYLASE lyase Lyase LYASE

  6. 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

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