Mercurial > repos > jjohnson > package_hmmer_3_0
comparison tool_dependencies.xml @ 0:3bc37773c609 draft default tip
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| author | jjohnson |
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| date | Thu, 05 Sep 2013 09:03:21 -0400 |
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| -1:000000000000 | 0:3bc37773c609 |
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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 $INSTALL_DIR</action> | |
| 8 <action type="shell_command">make</action> | |
| 9 <action type="shell_command">make check</action> | |
| 10 <action type="shell_command">make install</action> | |
| 11 <action type="set_environment"> | |
| 12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 13 </action> | |
| 14 </actions> | |
| 15 </install> | |
| 16 <readme> | |
| 17 HMMER is used to search sequence databases for homologs of protein sequences, and to make protein | |
| 18 sequence alignments. HMMER can be used to search sequence databases with single query sequences | |
| 19 but it becomes particularly powerful when the query is an multiple sequence alignment of a sequence family. | |
| 20 HMMER makes a profile of the query that assigns a position-specific scoring system for substitutions, | |
| 21 insertions, and deletions. HMMER profiles are probabilistic models called "profile hidden Markov models" | |
| 22 (profile HMMs) (Krogh et al., 1994; Eddy, 1998; Durbin et al., 1998). | |
| 23 | |
| 24 Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older | |
| 25 scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote | |
| 26 homologs, because of the strength of its underlying probability models. In the past, this strength came | |
| 27 at a significant computational cost, with profile HMM implementations running about 100x slower than | |
| 28 comparable BLAST searches. With HMMER3, HMMER is now essentially as fast as BLAST. | |
| 29 | |
| 30 The programs in HMMER:: | |
| 31 | |
| 32 Single sequence queries: new to HMMER3:: | |
| 33 | |
| 34 phmmer Search a sequence against a sequence database. (BLASTP-like) | |
| 35 jackhmmer Iteratively search a sequence against a sequence database. (PSIBLAST-like) | |
| 36 | |
| 37 Replacements for HMMER2's functionality:: | |
| 38 | |
| 39 hmmbuild Build a pro#le HMM from an input multiple alignment. | |
| 40 hmmsearch Search a pro#le HMM against a sequence database. | |
| 41 hmmscan Search a sequence against a pro#le HMM database. | |
| 42 hmmalign Make a multiple alignment of many sequences to a common pro#le HMM. | |
| 43 | |
| 44 Other utilities:: | |
| 45 | |
| 46 hmmconvert Convert pro#le formats to/from HMMER3 format. | |
| 47 hmmemit Generate (sample) sequences from a pro#le HMM. | |
| 48 hmmfetch Get a pro#le HMM by name or accession from an HMM database. | |
| 49 hmmpress Format an HMM database into a binary format for hmmscan. | |
| 50 hmmstat Show summary statistics for each pro#le in an HMM database | |
| 51 | |
| 52 ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf | |
| 53 </readme> | |
| 54 </package> | |
| 55 | |
| 56 </tool_dependency> |