Difference between revisions of "Missing RNA genes? 2009"
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1). We looked at the [http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&page=rnas&taxon_oid=2500575004&locus_type=xRNA two "other RNA" genes ] from last year's species ([http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2500575004 Halorhabdus utahensis AX-2, DSM 12940]) and compared those sequences to [ftp://ftp.jgi-psf.org/pub/JGI_data/Microbial/halomicrobium_mukohataei_DSM_12286/080213/4083000.fsa our species entire genome ] in two different manners: | 1). We looked at the [http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&page=rnas&taxon_oid=2500575004&locus_type=xRNA two "other RNA" genes ] from last year's species ([http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2500575004 Halorhabdus utahensis AX-2, DSM 12940]) and compared those sequences to [ftp://ftp.jgi-psf.org/pub/JGI_data/Microbial/halomicrobium_mukohataei_DSM_12286/080213/4083000.fsa our species entire genome ] in two different manners: | ||
| − | A). [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=blast2seq Blast2] | + | A). [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=blast2seq Blast2 of ] |
and | and | ||
Revision as of 21:14, 31 August 2009
In looking for other RNA genes we did the following:
1). We looked at the two "other RNA" genes from last year's species (Halorhabdus utahensis AX-2, DSM 12940) and compared those sequences to our species entire genome in two different manners:
A). Blast2 of
and
B). Halomicrobium mukohataei genome portal
Results are as follows. . .
For "other RNA" gene 2500590731, named SRP_euk_arch, in the Halorhabdus utahensis AX-2, DSM 12940 genmone (820149..820441 (-)(293bp)):
2). We also looked to ensure that all 20 amino acids had an associated tRNA gene encoded and all 20 amino acids were represented (although at varying frequencies).
In the future we would like to. . .
1). Compare our species to very closely related species that have been annotated for "other RNA genes"
2). Determine what "other RNA" genes we should be looking for in archae specifically.
