Mercurial > repos > iuc > package_hmmer_3_0
comparison tool_dependencies.xml @ 0:bae6be83ada5 draft default tip
Initial uploaded, developed from Jim Johnson
author | iuc |
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date | Wed, 09 Oct 2013 09:55:39 -0400 |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="hmmer" version="3.0"> | |
4 <install version="1.0"> | |
5 <actions> | |
6 <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz</action> | |
7 <action type="shell_command">./configure --prefix $INSTALL_DIR</action> | |
8 <action type="shell_command">make</action> | |
9 <action type="shell_command">make install</action> | |
10 <action type="set_environment"> | |
11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
12 </action> | |
13 </actions> | |
14 </install> | |
15 <readme> | |
16 HMMER is used to search sequence databases for homologs of protein sequences, and to make protein | |
17 sequence alignments. HMMER can be used to search sequence databases with single query sequences | |
18 but it becomes particularly powerful when the query is an multiple sequence alignment of a sequence family. | |
19 HMMER makes a profile of the query that assigns a position-specific scoring system for substitutions, | |
20 insertions, and deletions. HMMER profiles are probabilistic models called "profile hidden Markov models" | |
21 (profile HMMs) (Krogh et al., 1994; Eddy, 1998; Durbin et al., 1998). | |
22 | |
23 Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older | |
24 scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote | |
25 homologs, because of the strength of its underlying probability models. In the past, this strength came | |
26 at a significant computational cost, with profile HMM implementations running about 100x slower than | |
27 comparable BLAST searches. With HMMER3, HMMER is now essentially as fast as BLAST. | |
28 | |
29 The programs in HMMER:: | |
30 | |
31 Single sequence queries: new to HMMER3:: | |
32 | |
33 phmmer Search a sequence against a sequence database. (BLASTP-like) | |
34 jackhmmer Iteratively search a sequence against a sequence database. (PSIBLAST-like) | |
35 | |
36 Replacements for HMMER2's functionality:: | |
37 | |
38 hmmbuild Build a pro#le HMM from an input multiple alignment. | |
39 hmmsearch Search a pro#le HMM against a sequence database. | |
40 hmmscan Search a sequence against a pro#le HMM database. | |
41 hmmalign Make a multiple alignment of many sequences to a common pro#le HMM. | |
42 | |
43 Other utilities:: | |
44 | |
45 hmmconvert Convert pro#le formats to/from HMMER3 format. | |
46 hmmemit Generate (sample) sequences from a pro#le HMM. | |
47 hmmfetch Get a pro#le HMM by name or accession from an HMM database. | |
48 hmmpress Format an HMM database into a binary format for hmmscan. | |
49 hmmstat Show summary statistics for each pro#le in an HMM database | |
50 | |
51 ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf | |
52 </readme> | |
53 </package> | |
54 | |
55 </tool_dependency> |