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I wonder difference among the gene database

I want to talk about the gene db, especially Refseq, Ensembl, UCSC

I wonder what they have merits and demerits, and what is difference among them.

ucsc ensembl refseq gene-db
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updated by emmajosenl • emmajosenl • written by science0530 • science0530

Well this depends on the information you are hoping to retrieve. Maybe if you say something about what you are hoping to find there, what your field of research is, what is your background (are you good in Perl - for ex.). then, maybe, I could provide some pros and cons for you.

cheers

mxs

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updated by Ram Ram • written by mxs mxs

I am a bioinformatician. I am working on a gene prediction project and want to do the homologous gene prediction. I have gone through the genomescan manual and I would like to implement that tool in my project. But there is no available links to download the file.

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written by emmajosenl • emmajosenl

Please write this as a new question as it is not an answer to this question.

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written by Emily Emily

1 answer

  • RefSeq sequences of lowest status of curation (Model) are derived from predictions of Genomescan, while the Ensembl pipeline uses a combination of the Genewise and Exonerate.
  • Since no gene prediction programs to date predict the exact same gene set, it is perhaps not surprising that an increase in the number of Model sequences is accompanied by an increase in unique sequences.
  • It seems likely that the inconsistencies of the gene predictions programmes are causing important discrepancies in the databases. Another source of the differences could be the differing criteria for transcription evidence for predicted genes.

Refer:

Larsson, Thomas P., et al. "Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery." FEBS letters 579.3 (2005): 690-698.

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updated by Ram Ram • written by Felix Francis Felix Francis

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