searching for gene sequences, automated

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    • #16666
      poloke
      Participant

      Hallo all,

      Recently I sequenced 3 pieces of DNA , now its pretty easy to check for similar genes in the ncbi databank: you just enter your sequence and you search… and you repeat this 3 times, since I had 3 genes.. However , what if someone has for example 300 genes to check?

      Is their any option to automate this proces?
      I am not an expert in bio-informatics and the use of the ncbi database, but I think it should be possible to automate this proces?
      Eg: if someone sequences an entirely new genome, I can hardly imagine they manually enter each contig in the website and search for it…

      Are their programs out there to automate this?

    • #111785
      canalon
      Participant

      Yes a lot.
      If you look in the NCBI bookshelf they will explain you how to program that for yourself, and many if not most DNA analysis package do provide that option.

    • #111787
      poloke
      Participant

      Do you have a specific link for it? I can go to the bookshelf, but those are just books, isnt there an online tutorial or something like that?
      Or perhaps you know some programs that are easy to use?

    • #111800
      canalon
      Participant

      Geneious is great if you have a few thousand dollars that do not know how to use 🙁
      I do not know of any free program doing that, but that is more likely a product of my ignorance.

      As for what book in the bookshelf, I do not which one for sure, but it is likely one of those: http://www.ncbi.nlm.nih.gov/books?term=pubmed

    • #111801
      poloke
      Participant

      As a student, I do not have thousands of dollars to spend :p

    • #111816
      JackBean
      Participant

      Even the BLAST @ NCBI web page gives you the opportunity to search with several sequences at once (I’m not aware what’s the limit, maybe 20 or 200 sequences;)

    • #112071
      poloke
      Participant
      quote JackBean:

      Even the BLAST _at_ NCBI web page gives you the opportunity to search with several sequences at once (I’m not aware what’s the limit, maybe 20 or 200 sequences;)

      I seem to have overlooked this, where can you find this?
      Can I simple add multiple sequences then? How do I seperate them when inserting multiple sequences?

    • #112081
      JackBean
      Participant

      yes, just put them in in FASTA format:
      >sequence 1 titel
      SEQUENCE1SEQUENCE
      STILLSEQUENCE1ETCETC
      >sequence 2 ID
      SEQUENCE2SEQUENCE AND THIS
      CANGOONAND
      ONANDONANDON:)
      >sequence 3
      ANDTHELASTONEBLAHBLAHBLAH

      or inserting simply several NCBI IDs if you have them

    • #112145
      triton
      Participant

      you can download ncbi database into your computer, install command line blast and do your search in you computer. You can have as many sequences as your processor tolerate. alternatively you can create an account in BIOPORTAL OSLO and use their cluster for blasting. You can submit milions of sequences in one file.

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