Several organism at NCBI have sequenced genome but no predictions of proteins. For example Caenorhabditis japonica genome is there but the NCBI ftp also lacks its proteome. What should I do to get proteome of this:
1. Should I train any gene prediction software to create gene models then getting proteins from that
2. Should I translate the available nucleotides
3. Any other method?
You can use any gene prediction software, to get the putative genes. The putative ORFs can then be converted into proteins for annotation.
Hi Ashmit,
Once a genome is sequenced, there is a very high chance that the list of predicted / encoded proteins is also provided in a database.
When thinking about organism specific proteomes it is a very good idea to have a look at uniprot (http://www.uniprot.org/). The website is the front of a powerful platform for protein centric information. Most importantly the data is extensively cross-referenced with other genome based resources and curation projects.
Specifically, the organism Caenorhabditis japonica has its defined (with up to date available information) proteome here: http://www.uniprot.org/proteomes/UP000005237 ( you can refer to the proteome ID, UP000005237, as it is stable).
Currently there are around 35000 proteins derived from the assembled genome:
http://www.uniprot.org/uniprot/?query=proteome:UP000005237
Ilian
Thanks Ilian, but what should we do if the proteome is also not available in any third-party databases.
Then one would need to perform open reading frame analysis and come up with potential coding genes. On algorithm that can be used for this (and is used by the Ensembl project) is GENSCAN:
https://en.wikipedia.org/wiki/GENSCAN.
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