gribskov@FCRFV1.NCIFCRF.GOV ("Gribskov, Michael") (11/20/90)
Will Fischer asked >Can anyone out there point me to a table of codon usages for >SEA URCHIN EGGS? For that matter, how about a good public-domain >or shareware program for generating same? It will be easier to respond to this question if we can get a little more detail. For instance, what kind of sea urchin? The literature includes sequences from Parechinus angulosus, Echinolampas crassa, Strongylocentrotus purpuratus*, Lytechinus pictus*, Psammechinus miliaris*, arbacia punctulata, Lytechinus variegatus*, Strongylocentrotus franciscanus, and probably others, although significant amounts of sequence information seems to be available only for those followed by '*'s. Are you interested in overall codon usage, or usage of highly expressed genes? Are you interested in codon usage of genes expressed only in early development (i.e. eggs), or at any time in the life cycle? Michael Gribskov gribskov@ncifcrf.gov
wmf%caat@LANL.GOV (Will Fischer) (11/21/90)
I previously asked >>Can anyone out there point me to a table of codon usages for >>SEA URCHIN EGGS? For that matter, how about a good public-domain >>or shareware program for generating same? Don Gilbert said >It just so happens that I made a sea urchin codon table for >people at iu. You can get it from anon. ftp to iubio.bio.indiana.edu, >cd [archive.molbio.data], get SEA-URCHIN.CODON-GCG. > >I had a codon table maker hacked from GCG software but it broke with >the new feature table format of GenBank. Mark Gunnell generated and sent tables: > I've enclosed three codonfrequency tables generated by the GCG program >CodonFrequency. These sequences were initially found in by scanning several >nucleotide databases [GenBank-65,EMBL-24,PirNuc-36], with DocSearch, a string >matching program, looking for the terms "Coding" or "CDS" and "Sea" and >"Urchin" and "Egg". Michael Gribskov asked in response: >It will be easier to respond to this question if we can get a little >more detail. For instance, what kind of sea urchin? > ... >Are you interested in overall codon usage, or usage of highly expressed >genes? Are you interested in codon usage of genes expressed only >in early development (i.e. eggs), or at any time in the life cycle? First, the disclaimer -- I got this request from "outside" my workplace (GenBank), and posted this note hoping to get a response so I could give these people *some* help. I have since found out more about the question... A researcher (haven't asked if I can name him, so I won't) isolated a peptide from Strongylocentrotus purpuratus eggs. Apparently it is expressed in other tissues as well, and in other organisms. Having partially sequenced the peptide, he wanted to synthesize oligos for PCR primers... I don't know what the best approach would be, other than using just the known S.purpuratus egg codons to generate the primers; if there are other opinions out there, I'd like to hear them (I am NO wet-bench biologist). Thanks to those who replied, if anyone else cares to, thanks in advance. -- Will Fischer INTERNET: wmf@caat.lanl.gov VOICE: 505-665-2177 FAX: 505-665-3493 US-MAIL: GenBank Annotation Group T-10, MS K710 Los Alamos National Laboratory Los Alamos, NM 87501