Blocks Searcher Email Server Options

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

Please note: The default output option (#OU) will change from OLD to ALL effective 1 July 2000. You may need to modify your procedures.

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:

#SQ
sequence in fasta or other common formats

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