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README.txt
domtab_30_hmmscan_001.out
domtab_30_hmmscan_002.out
domtab_30_hmmscan_003.out
domtab_30_hmmscan_004.out
domtab_30_hmmsearch_001.out
domtab_31b1_hmmscan_001.out
domtab_31b1_hmmsearch_001.out
tab_30_hmmscan_001.out
tab_30_hmmscan_002.out
tab_30_hmmscan_003.out
tab_30_hmmscan_004.out
tab_31b1_hmmscan_001.out
tab_31b1_hmmsearch_001.out
text_20_hmmsearch_001.out
text_21_hmmpfam_001.out
text_22_hmmpfam_001.out
text_22_hmmsearch_001.out
text_23_hmmpfam_001.out
text_23_hmmpfam_002.out
text_23_hmmpfam_003.out
text_24_hmmpfam_001.out
text_30_hmmscan_001.out
text_30_hmmscan_002.out
text_30_hmmscan_003.out
text_30_hmmscan_004.out
text_30_hmmscan_005.out
text_30_hmmscan_006.out
text_30_hmmscan_007.out
text_30_hmmscan_008.out
text_30_hmmscan_009.out
text_30_hmmscan_010.out
text_30_hmmsearch_001.out
text_30_hmmsearch_002.out
text_30_hmmsearch_003.out
text_30_hmmsearch_004.out
text_30_hmmsearch_005.out
text_31b1_hmmscan_001.out
text_31b1_hmmsearch_001.out
text_31b2_hmmscan_001.out
text_31b2_hmmsearch_001.out
text_31b2_hmmsearch_002.out
text_31b2_phmmer_001.out

README.txt

HMMER TEST DATA FILES
=====================

This directory contains various data files for testing the
HMMER-related code in Biopython.


HMMER3 OUTPUT FILES (plain text)
-------------------------------
text_31b2_hmmscan_001.out    single query, multiple hits, some hits have no hsps (issue #525)
text_31b1_hmmscan_001.out    multiple queries
text_30_hmmscan_001.out      multiple queries
text_30_hmmscan_002.out      single query, no match
text_30_hmmscan_003.out      single query, one match, one hsp per match
text_30_hmmscan_004.out      single query, multiple matches, one hsp per match
text_30_hmmscan_005.out      single query, multiple matches, multiple hsps per match
text_30_hmmscan_006.out      single query, multiple matches, multiple hsps per match, inclusion threshold present
text_30_hmmscan_007.out      single query, one match, no alignment
text_30_hmmscan_008.out      single query, multiple matches, no alignment width
text_30_hmmscan_009.out      single query, alignment block(s) with large gaps (bug 3399 in Redmine)
text_30_hmmscan_010.out
text_31b1_hmmsearch_001.out  multiple queries
text_30_hmmsearch_001.out    single query, no match
text_30_hmmsearch_002.out    single query, multiple matches, multiple hsps per match
text_30_hmmsearch_003.out    single query, multiple matches, multiple hsps per match, no alignment
text_30_hmmsearch_004.out    single query, multiple matches, multiple hsps per match, no alignment width
text_30_hmmsearch_005.out    multiple queries
text_31b2_phmmer_001.out     multiple queries, with -A flag (issue #588)
text_31b2_hmmsearch_001.out  single query, comment lines after query section (issue #1126)
text_31b2_hmmsearch_002.out  multiple queries, multiple comment lines after query section (issue #1126)

tab_31b1_hmmscan_001.out    multiple queries
tab_30_hmmscan_001.out      multiple queries
tab_30_hmmscan_002.out      single query, no match
tab_30_hmmscan_003.out      single query, one match, one hsp per match
tab_30_hmmscan_004.out      single query, multiple matches, one hsp per match
tab_31b1_hmmsearch_001.out  single query, multiple matches, one hsp per match

domtab_31b1_hmmscan_001.out     multiple queries
domtab_30_hmmscan_001.out       multiple queries, hmm as hit
domtab_30_hmmscan_002.out       single query, no match, hmm as hit
domtab_30_hmmscan_003.out       single query, one match, one hsp per match, hmm as hit
domtab_30_hmmscan_004.out       single query, multiple matches, one hsp per match, hmm as hit
domtab_31b1_hmmsearch_001.out
domtab_30_hmmsearch_001.out     single query, multiple matches, hmm as query


HMMER2 OUTPUT FILES (plain text)
--------------------------------
text_21_hmmpfam_001.out     single query, two matches, bioperl's hmmpfam.out file
text_22_hmmpfam_001.out     single query, one match, bioperl's L77119.hmmer file
text_23_hmmpfam_001.out     single query, multiple matches, bioperl's hmmpfam_cs.out file
text_23_hmmpfam_002.out     single query, no match
text_23_hmmpfam_003.out     single query, one match, missing some consensus content
text_24_hmmpfam_001.out     multiple queries
text_20_hmmsearch_001.out   single query, multiple matches, bioperl's hmmsearch.out file
text_22_hmmsearch_001.out   single query, multiple matches, bioperl's cysprot1b.hmmsearch file