Transcript Workshop practical

Workshop practical
Helsinki Workshop
September 2006
Initial setup
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Log in and checkout the biomart perl code:
cvs -d :pserver:[email protected]:/cvsroot/CVSmaster login
cvs -d :pserver:[email protected]:/cvsroot/CVSmaster co
biomart-web
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Add the biomart-web/lib/BioMart directory to your PERL5LIB.
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Install the Exception::Class and XML::Simple modules from CPAN.
perl -MCPAN -e shell
install XML::Simple Exception::Class
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Run the example API script to check everything is installed correctly:
perl biomart-web/scripts/new_0_5_exampleSimple.pl
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Run the webservices example:
perl biomart-web/script/webExample.pl Query.xml
API exercises
Write API scripts to perform the following tasks:
(1)
Recover the gene and transcript stable IDs along with the
chromosome name for human Ensembl genes on chromosome 1.
(2)
Further narrow down (1) to only genes between positions 1p36.33
and 1q12 .
(3)
Recover the gene and transcript stable IDs and HGNC symbol
identifier for human Ensembl genes that match a HGNC symbol of
FGFR1, IL2 or DERL3.
(4)
For the same genes as in (3) recover the peptide sequence with
Ensembl gene and transcript stable Ids as header attributes in FASTA
output format.
(5)
Recover the human gene stable ID, human transcript stable ID,
human chromosome, mouse gene stable ID, mouse transcript stable
ID and mouse chromosome for human, chromosome 1 Ensembl genes
with a mouse ortholog on mouse chromosome 2.
Martservice exercises
Write Query XMLs and run with webExample.pl to perform the same tasks:
(1)
Recover the gene and transcript stable IDs along with the chromosome name
for human Ensembl genes on chromosome 1.
(2)
Further narrow down (1) to only genes between positions 1p36.33 and 1q12 .
(3)
Recover the gene and transcript stable IDs and HGNC symbol identifier for
human Ensembl genes that match a HGNC symbol of FGFR1, IL2 or DERL3.
(4)
For the same genes as in (3) recover the peptide sequence with Ensembl gene
and transcript stable Ids as header attributes in FASTA output format.
(5)
Recover the human gene stable ID, human transcript stable ID, human
chromosome, mouse gene stable ID, mouse transcript stable ID and mouse
chromosome for human, chromosome 1 Ensembl genes with a mouse ortholog
on mouse chromosome 2.