BLAST search against a EST database
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9.0 years ago
zizigolu ★ 4.3k

I am going to do a blast search against a EST database, which I should select in menu, unigene, CDS, transcripts or scafolds?

Thanks

blast • 4.1k views
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What do you actually want to achieve - citrus ORF identification or something else?

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I want to find the key genes involved in a specific pathway, by blast and keyword search against EST database then blast the result against genebank to filter the results

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9.0 years ago
cdsouthan ★ 1.9k

You can select "Expressed Sequence Tags (est)" on the NCBI BLAST menu

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But I am not in NCBI, I am working with citrus genome database and in menu there are just the options I mentioned above. you think is the unigene same est?

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9.0 years ago

You have several choices..

If Internet connection is available..

  1. If you are in the internet, you can go to NCBI Blast and select the EST database..
  2. Then, using megablast or dc-megablast run your comparison
  3. If not hits are obtained, then you can make a search in the SRA database. If hits are found for the citrus genome, then you can write down the accession SRA numbers, and go again to the NCBI to select those databases (in this case the latest option of the databases is the SRA database itself)

If not internet connection is available thing are pretty much complicated. You need to run your search locally, but you need to get your programs and data from the internet

  1. Somehow look for the blast+ programs that can be downloaded for unix, Mac and Windows systems
  2. Look for the sratoolkits. Read a little bit about it. There is an option that allows you to run megablast and dc-megablast locally (in your own PC) with the same SRA files you download from the SRA database. Not need neither to create FastQ or Fasta files, not to create a database with these files. Is pretty simple
  3. If you have your own data. then you can run blast locally creating a database with makeblasdb, and then define with task what you want to run with blastn (megablast or discontinuous megablast), etc
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You can create the local database with your EST library using the latest option. I will go for everything you have in that EST library

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Thanks Antonio, I am with my PC connected to internet

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