Workshop practical

1
Workshop practical

• Helsinki Workshop
• September 2006

2
Initial setup

• Log in and checkout the biomart perl code
• cvs -d pservercvsuser_at_cvs.sanger.ac.uk/cvsroot
  /CVSmaster login
• cvs -d pservercvsuser_at_cvs.sanger.ac.uk/cvsroot
  /CVSmaster co biomart-web
• Add the biomart-web/lib/BioMart directory to your
  PERL5LIB.
• Install the ExceptionClass and XMLSimple
  modules from CPAN.
• perl -MCPAN -e shell
• install XMLSimple ExceptionClass
• Run the example API script to check everything is
  installed correctly
• perl biomart-web/scripts/new_0_5_exampleSimple.pl
• Run the webservices example
• perl biomart-web/script/webExample.pl Query.xml

3
API exercises

• Write API scripts to perform the following tasks
• Recover the gene and transcript stable IDs along
  with the chromosome name for human Ensembl genes
  on chromosome 1.
• Further narrow down (1) to only genes between
  positions 1p36.33 and 1q12 .
• 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.
• 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.
• 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.

4
Martservice exercises

• Write Query XMLs and run with webExample.pl to
  perform the same tasks
• Recover the gene and transcript stable IDs along
  with the chromosome name for human Ensembl genes
  on chromosome 1.
• Further narrow down (1) to only genes between
  positions 1p36.33 and 1q12 .
• 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.
• 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.
• 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.