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The use of local blast+

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  • The use of local blast+

    Hi ,
    i would like to use all the features of BLAST+ to create my local blast software ,I have some problem to use filter an masking function .
    The SEG program is used to mask or filter low complexity regions in amino acid queries. The DUST program is used to mask or filter such regions in nucleic acid queries.

    which parameter is corresponding to "Mask for lookup table only " ??and which for "Species-specific repeats filter for:"?

    thanks!

  • #2
    The following options should be the ones you want, especially the latter option.

    -gilist <String>
    Restrict search of database to list of GI's

    -seqidlist <String>
    Restrict search of database to list of SeqId's

    -negative_gilist <String>
    Restrict search of database to everything except the listed GIs

    -entrez_query <String>
    Restrict search with the given Entrez query

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    • #3
      Originally posted by westerman View Post
      The following options should be the ones you want, especially the latter option.

      -gilist <String>
      Restrict search of database to list of GI's

      -seqidlist <String>
      Restrict search of database to list of SeqId's

      -negative_gilist <String>
      Restrict search of database to everything except the listed GIs

      -entrez_query <String>
      Restrict search with the given Entrez query
      thanks for you answer,but i have some different idea, "Filters and Masking" is used for the query sequence ,but the "gilist " is used for the database.

      do you know where and how to use the two parameters :
      -filtering_db <String>
      BLAST database containing filtering elements (i.e.: repeats)

      -soft_masking <Boolean>
      Apply filtering locations as soft masks
      Default = `true'
      thank you very much!

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