* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Workshop practical
Genetic engineering wikipedia , lookup
Epigenetics of diabetes Type 2 wikipedia , lookup
Essential gene wikipedia , lookup
Human genetic variation wikipedia , lookup
Saethre–Chotzen syndrome wikipedia , lookup
Segmental Duplication on the Human Y Chromosome wikipedia , lookup
Copy-number variation wikipedia , lookup
Pathogenomics wikipedia , lookup
Public health genomics wikipedia , lookup
Gene therapy wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Nutriepigenomics wikipedia , lookup
Human genome wikipedia , lookup
Epigenetics of neurodegenerative diseases wikipedia , lookup
Long non-coding RNA wikipedia , lookup
Minimal genome wikipedia , lookup
Genome evolution wikipedia , lookup
Polycomb Group Proteins and Cancer wikipedia , lookup
Biology and consumer behaviour wikipedia , lookup
History of genetic engineering wikipedia , lookup
Gene nomenclature wikipedia , lookup
Ridge (biology) wikipedia , lookup
Gene desert wikipedia , lookup
Skewed X-inactivation wikipedia , lookup
Genomic imprinting wikipedia , lookup
Gene expression programming wikipedia , lookup
Neocentromere wikipedia , lookup
Y chromosome wikipedia , lookup
Microevolution wikipedia , lookup
Gene expression profiling wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Designer baby wikipedia , lookup
Workshop practical Helsinki Workshop September 2006 Initial setup - 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 - Add the biomart-web/lib/BioMart directory to your PERL5LIB. - Install the Exception::Class and XML::Simple modules from CPAN. perl -MCPAN -e shell install XML::Simple Exception::Class - 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 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.