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Merge pull request #17 from Rfam/update-12p2-infernal-genome-annot
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Updates genome annotation section for 12.2.
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@AntonPetrov
AntonPetrov committed Mar 14, 2017
2 parents ea127d2 + 34bc352 commit 67ad4c3
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22 changes: 14 additions & 8 deletions docs/source/genome-annotation.rst
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Expand Up @@ -63,15 +63,22 @@ you can use the executable files in *easel/miniapps/*. To install them::
For more information on customizing the Infernal installation, see
section 2 of the `Infernal User's Guide <http://eddylab.org/infernal/Userguide.pdf>`_.

2. Download the Rfam library of CMs from `<ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz>`_.
2. Download the Rfam library of CMs from
`<ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam.cm.gz>`_ and the
Rfam claninfo file from
`<ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam12.2.claninfo>`_ .


::

$ wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz
$ wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam.cm.gz
$ gunzip Rfam.cm.gz
$ wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam12.2.claninfo

If you do not have ``wget`` installed and in your path, `download the
file <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz>`_ from a browser.
If you do not have ``wget`` installed and in your path, download the
files `<ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam.cm.gz>`_ and
`<ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam12.2.claninfo>`_
from a browser.

3. Use the Infernal program cmpress to index the Rfam.cm file

Expand Down Expand Up @@ -119,13 +126,12 @@ be used in step 5.

::

$ cmscan -Z 5.874406 --cut_ga --rfam --nohmmonly --tblout mrum-genome.tblout --fmt 2 --clanin testsuite/Rfam.12.1.clanin Rfam.cm tutorial/mrum-genome.fa > mrum-genome.cmscan
$ cmscan -Z 5.874406 --cut_ga --rfam --nohmmonly --tblout mrum-genome.tblout --fmt 2 --clanin Rfam12.2.claninfo Rfam.cm tutorial/mrum-genome.fa > mrum-genome.cmscan

.. note:: The above cmscan command assumes you are in the
infernal-1.1.2 directory from step 1. If not, you'll need to
supply the paths to the tutorial/mrum-genome.fa and
testsuite/Rfam.12.1.clanin files within the infernal-1.1.2
directory.
file within the infernal-1.1.2 directory.

Explanations of the command line options used in the above command are as follows:

Expand Down Expand Up @@ -156,7 +162,7 @@ Explanations of the command line options used in the above command are as follow

:``--clanin``:
Clan information should be read from the file
``testsuite/Rfam.12.1.claninfo``. This file lists which models belong
``Rfam12.2.claninfo``. This file lists which models belong
to the same clan. `Rfam clans <http://rfam.xfam.org/clans>`_
are groups of models that are homologous and
therefore it is expected that some hits to these models will
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30 changes: 15 additions & 15 deletions docs/source/mrum-genome.cmscan
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Expand Up @@ -10,7 +10,7 @@
# tabular output format: 2
# model-specific thresholding: GA cutoffs
# Rfam pipeline mode: on [strict filtering]
# clan information read from file: /Users/nawrockie/src/infernal-1.1.2/testsuite/Rfam.12.1.clanin
# clan information read from file: Rfam12.2.claninfo
# HMM-only mode for 0 basepair models: no
# number of worker threads: 8
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Expand Down Expand Up @@ -3569,19 +3569,19 @@ Hit alignments:
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (5874406 residues searched)
Query sequences re-searched for truncated hits: 1 (718.7 residues re-searched, avg per model)
Target model(s): 2473 (308563 consensus positions)
Windows passing local HMM SSV filter: 13142153 (0.1571); expected (0.06)
Windows passing local HMM Viterbi filter: 3721423 (0.04818); expected (0.02)
Windows passing local HMM Viterbi bias filter: 1437429 (0.0142); expected (0.02)
Windows passing local HMM Forward filter: 178792 (0.002382); expected (0.0002)
Windows passing local HMM Forward bias filter: 108341 (0.001552); expected (0.0002)
Windows passing glocal HMM Forward filter: 59142 (0.0008075); expected (0.0002)
Windows passing glocal HMM Forward bias filter: 49390 (0.0006423); expected (0.0002)
Envelopes passing glocal HMM envelope defn filter: 49667 (0.0003772); expected (0.0002)
Envelopes passing local CM CYK filter: 19981 (0.0001258); expected (0.0001)
Total CM hits reported: 78 (2.407e-06); includes 0 truncated hit(s)

# CPU time: 2472.23u 42.65s 00:41:54.88 Elapsed: 00:07:34.28
Query sequences re-searched for truncated hits: 1 (727.4 residues re-searched, avg per model)
Target model(s): 2588 (329475 consensus positions)
Windows passing local HMM SSV filter: 13657928 (0.1571); expected (0.06)
Windows passing local HMM Viterbi filter: 3879011 (0.04816); expected (0.02)
Windows passing local HMM Viterbi bias filter: 1485448 (0.01407); expected (0.02)
Windows passing local HMM Forward filter: 186053 (0.002372); expected (0.0002)
Windows passing local HMM Forward bias filter: 112532 (0.001546); expected (0.0002)
Windows passing glocal HMM Forward filter: 61287 (0.0008004); expected (0.0002)
Windows passing glocal HMM Forward bias filter: 50940 (0.0006329); expected (0.0002)
Envelopes passing glocal HMM envelope defn filter: 51296 (0.0003729); expected (0.0002)
Envelopes passing local CM CYK filter: 20443 (0.0001228); expected (0.0001)
Total CM hits reported: 78 (2.3e-06); includes 0 truncated hit(s)

# CPU time: 2726.89u 52.11s 00:46:19.00 Elapsed: 00:08:37.16
//
[ok]
6 changes: 3 additions & 3 deletions docs/source/mrum-genome.tblout
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Expand Up @@ -14,7 +14,7 @@
12 SSU_rRNA_eukarya RF01960 NC_013790.1 - CL00111 cm 1 1851 760878 762348 + no 1 0.54 4.5 963.8 9.9e-291 ! = 8 1.000 0.998 " " " -
13 SSU_rRNA_microsporidia RF02542 NC_013790.1 - CL00111 cm 1 1312 2043361 2041891 - no 1 0.53 4.6 919.9 7.7e-281 ! = 7 1.000 0.998 " " " -
14 SSU_rRNA_microsporidia RF02542 NC_013790.1 - CL00111 cm 1 1312 760878 762348 + no 1 0.54 4.5 917.2 5.4e-280 ! = 8 1.000 0.998 " " " -
15 RNaseP_arch RF00373 NC_013790.1 - - cm 1 303 2614544 2614262 - no 1 0.43 0.0 184.9 1.1e-53 ! * - - - - - - -
15 RNaseP_arch RF00373 NC_013790.1 - CL00002 cm 1 303 2614544 2614262 - no 1 0.43 0.0 184.9 1.1e-53 ! * - - - - - - -
16 Archaea_SRP RF01857 NC_013790.1 - CL00003 cm 1 318 1064321 1064634 + no 1 0.44 0.1 197.6 6.9e-49 ! * - - - - - - -
17 FMN RF00050 NC_013790.1 - - cm 1 140 193975 193837 - no 1 0.42 0.0 115.2 6.8e-28 ! * - - - - - - -
18 tRNA RF00005 NC_013790.1 - CL00001 cm 1 71 735136 735208 + no 1 0.59 0.0 72.1 4.9e-16 ! * - - - - - - -
Expand Down Expand Up @@ -84,7 +84,7 @@
# Pipeline mode: SCAN
# Query file: /Users/nawrockie/src/infernal-1.1.2/tutorial/mrum-genome.fa
# Target file: Rfam.cm
# Option settings: cmscan -Z 5.874406 --tblout mrum-genome.tblout --fmt 2 --cut_ga --rfam --nohmmonly --clanin /Users/nawrockie/src/infernal-1.1.2/testsuite/Rfam.12.1.clanin Rfam.cm /Users/nawrockie/src/infernal-1.1.2/tutorial/mrum-genome.fa
# Option settings: cmscan -Z 5.874406 --tblout mrum-genome.tblout --fmt 2 --cut_ga --rfam --nohmmonly --clanin Rfam12.2.claninfo Rfam.cm /Users/nawrockie/src/infernal-1.1.2/tutorial/mrum-genome.fa
# Current dir: /Users/nawrockie/Dropbox/work/notebook/16_1111_rfam_docs_inf_genome_annotation
# Date: Fri Nov 18 09:19:31 2016
# Date: Tue Mar 14 12:33:23 2017
# [ok]

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