Difference between revisions of "Genome comparisons"

Revision as of 16:22, 27 October 2009

We would like to edit the Perl tool that currently compares start and stop codons from the same species in three different annotations, or find an existing tool that will do the following: We would like this tool to compare our Halomicrobium mukohataei genome to 9 other halophile’s genomes all using the annotations from RAST. Basically, the Perl script should take all the known H. mukohataei amino acid sequences from RAST and compare these (in a Blastp manner) to all 9 other halophile genomes. In this manner, we will be able to determine which genes in H. mukohataei are conserved among other halophiles and which are unique to this species. The other 9 species we would like to compare are:
Haloarcula sp 33799 (Karen)
Haloarcula sp 33800
Haloarcula vallismortis (Megan)
Haloferax denitrificans (Megan)
Haloferax mediterranei (Claudia)
Haloferax mucosum (Sarah)
Haloferax sulfurifontis (Sarah)
Haloferax volcanii (Sarah)
Halorhabdus utahensis (Karen)

The complete amino acid sequences for each of these species will be needed to do this comparison. A link to each of these sequences can be found below:

Halomicrobium mukohataei FASTA sequence
Haloarcula sp 33799 FASTA sequence
Haloarcula sp 33800 FASTA sequence
Haloarcula vallismortis FASTA sequence
Haloferax denitrificans FASTA sequence
Haloferax mediterranei FASTA sequence
Haloferax mucosum FASTA sequence
Haloferax sulfurifontis FASTA sequence
Haloferax volcanii FASTA sequence
Halorhabdus utahensis FASTA sequence