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4.1 Put

Parameters accepted by the 'Put' command are listed in the table below. Not all are manditory. Certain parameters only work with a subset of other parameters in the list. The 'Put' command will send parameters included within the URL to Blast.cgi, which will be used to customized the search request.

Table 4.2 Parameters for Command Put
ALIGNMENTS (5.1.1) BLAST_PROGRAMS (5.1.3) CDD_SEARCH (5.1.4)
COMPOSITION_BASED_STATISTICS (5.1.6) DATABASE_PREFIX (5.1.9) DATABASE (5.1.7)
DB_GENETIC_CODE (5.1.10) DESCRIPTIONS (5.1.11) ENTREZ_QUERY (5.1.13)
EXPECT (5.1.14) FILTER (5.1.18) GAPCOSTS (5.1.22)
GENETIC_CODE (5.1.23) HITLIST_SIZE (5.1.25) I_THRESH (5.1.27)
LCASE_MASK (5.1.28) MATCH_SCORES (5.1.31) MATRIX_NAME (5.1.32)
MAX_NUM_SEQ (5.1.34) MEGABLAST (5.1.34) NUM_OVERVIEW (5.1.39)
OTHER_ADVANCED (5.1.40) PERC_IDENT (5.1.42) PHI_PATTERN (5.1.43)
PROGRAM (5.1.44) PSSM (5.1.45) QUERY (5.1.46)
QUERY_BELIEVE_DEFLINE (5.1.47) QUERY_FROM (5.1.48) QUERY_TO (5.1.49)
REPEATS (5.1.50) SHORT_QUERY_ADJUST (5.1.54) SEARCHSP_EFF (5.1.53)
TEMPLATE_LENTH (5.1.58) TEMPLATE_TYPE (5.1.59) THRESHOLD (5.1.60)
TWO_HITS (5.1.61) WORD_SIZE (5.1.62) WWW_BLAST_TYPE (5.1.63)

In the example below, we are to search the input query using blastp, with the low complexity filter, against the protein nr database. We set the maximum number of alignments and descriptions to display in the result to 100:

$ lynx -source "\

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put\

&QUERY=SSWWAHVEMGPPDPILGVTEAYKRDTNSKK&PROGRAM=blastp&FILTER=L\

&DATABASE=nr&ALIGNMENTS=100&DESCRIPTIONS=100"


next up previous contents index
Next: 4.2 Get Up: 4 Commands Previous: 4 Commands   Contents   Index
Tao Tao 2007-08-03