# Blocks Searcher Email Server Options

Please note: The Blocks Searcher Email Server will soon be discontinued. For searching a few queries, supply your email address on the Block Searcher form. Here is a sample perl script to do bulk searches.

Blocks Email Searcher: blocks@blocks.fhcrc.org
Examples of the new options follow.

Please note: Please send clear text only.

Please note: Effective 2 May 2002 the #SQ option is required.

Please note: Default options will be used if the message consists solely of a sequence.

Please note: If you want to put comments in the message, start them with # in the first column and put them before the sequence, being careful not to start your comment with any of the reserved words listed below. Nothing should follow the sequence.

Searching options:

- Database to search:

      #DB PLUS(default) | MINUS(PLUS without biased blocks) | PRINTS

- Query sequence type:

      #TY AUTO(default) | AA | DNA

- For DNA queries, strands to search:

      #ST BOTH(default) | FORWARD | REVERSE or   2 | 1 | -1

- For DNA queries, genetic code to use for translation:

      #GE 0(default) to 8

Post-processing options:

- Output type:

      #OU ALL(default) | SUM | GFF | OLD | RAW

- Output format:

      #FO TEXT(default) | HTML

- Expected value cutoff:

      #EX n (default=5)

Sequence definition (required):

    #SQ
    Sequence in fasta or other common formats.
    WARNING: Everything after #SQ is treated as sequence, so do not
    append any signature, etc.

Examples:

    1. Old defaults; result of just mailing sequence
    with no lines beginning with "#":
    #DB plus
    #TY auto
    #ST 2
    #GE 0
    #OU old
    #FO text
    #SQ
    >SPRE_RAT SEPIAPTERIN REDUCTASE (EC 1.1.1.153) (SPR)
    MEGGRLGCAV CVLTGASRGF GRALAPQLAG LLSPGSVLLL SARSDSMLRQ LKEELCTQQP
    GLQVVLAAAD LGTESGVQQL LSAVRELPRP ERLQRLLLIN NAGTLGDVSK GFLNINDLAE
    VNNYWALNLT SMLCLTTGTL NAFSNSPGLS KTVVNISSLC ALQPFKGWGL YCAGKAARDM
    LYQVLAVEEP SVRVLSYAPG PLDTNMQQLA RETSMDPELR SRLQKLNSEG ELVDCGTSAQ
    KLLSLLQRDT FQSGAHVDFY DI

    2. New searching/post-processing defaults
    #DB plus
    #TY auto
    #ST 2
    #GE 0
    #EX 5
    #OU all
    #FO text
    #SQ
    >SPRE_RAT SEPIAPTERIN REDUCTASE (EC 1.1.1.153) (SPR)
    MEGGRLGCAV CVLTGASRGF GRALAPQLAG LLSPGSVLLL SARSDSMLRQ LKEELCTQQP
    GLQVVLAAAD LGTESGVQQL LSAVRELPRP ERLQRLLLIN NAGTLGDVSK GFLNINDLAE
    VNNYWALNLT SMLCLTTGTL NAFSNSPGLS KTVVNISSLC ALQPFKGWGL YCAGKAARDM
    LYQVLAVEEP SVRVLSYAPG PLDTNMQQLA RETSMDPELR SRLQKLNSEG ELVDCGTSAQ
    KLLSLLQRDT FQSGAHVDFY DI

    3. New searching/post-processing options
    #DB prints
    #TY DNA
    #ST 1
    #GE 1
    #EX 3
    #OU sum
    #FO html
    #SQ
    gi|8133541|gb|AW507376.1|AW507376 EST00092 Rattus
    ACATCATGGCTCTGACTTGGGTTAAGCTCTTGGCACCAATGTCCTGACAGGAATGCTGGATGCCAGCAAT
    CAAATAAGGGACAAACTTGTGGATAGACCCTTTGTCCTGCACTGCCCCTGAAACTCCTTGGGCCACTTTG
    ATCTTGTCAGCTTCACTGAAATATCGGTTCTGGCTGCTGAGGTGTTTGTCAAGTACATCAAGGAAAAATA
    CCCCAATCTCCAGGTCATCGGAGGCAATGTAGTCACTGCTGCTCAAGCCAAGAACCTCATCGACGCAGGT
    GTGGACGCTCTGCGAGTCGGCATGGGAAGTGGTTCCATCTGCATCACCCAGGAAGTGTTGGCCTGTGGGC
    GACCCCAAGCAACAGCAGTATACAAGGTCTCTGAGTATGCCCGTCGCTTCGGTGTCCCTGGTATTGCTGA
    TGGAGGAAT