1hmmpgmd(1)                       HMMER Manual                       hmmpgmd(1)
2
3
4

NAME

6       hmmpgmd  - daemon for searching a protein query against a protein data‐
7       base
8
9
10

SYNOPSIS

12       hmmpgmd [options]
13
14
15

DESCRIPTION

17       The hmmpgmd program is the  daemon  that  we  use  internally  for  the
18       hmmer.org  web  server,  and essentially stands in front of the protein
19       search programs phmmer, hmmsearch, and hmmscan.
20
21       To use hmmpgmd, first an instance  must  be  started  up  as  a  master
22       server,  and  provided  with at least one of a sequence database (using
23       the --seqdb flag) and/or an HMM database (using the --hmmdb  flag).   A
24       sequence  database must be in the hmmpgmd format, which may be produced
25       using esl-reformat.  An HMM database is of the form  produced  by  hmm‐
26       build.  The input database(s) will be loaded into memory by the master.
27       When the master has finished loading the  database(s),  it  prints  the
28       line: "Data loaded into memory. Master is ready."
29
30
31
32       Only  after  master  is  ready, one or more instances of hmmpgmd may be
33       started as workers. These workers may be (and typically are) on differ‐
34       ent machines from the master, but must have access to the same database
35       file(s) provided to the master, with the same path. As with the master,
36       each worker loads the database(s) into memory, and indicates completion
37       by printing: "Data loaded into memory. Worker is ready."
38
39
40
41       The master server and workers are expected to remain running.   One  or
42       more  clients  then  connect  to  the  master  and submit possibly many
43       queries. The master distributes the work of a query among the  workers,
44       collects  results, and merges them before responding to the client. Two
45       example client programs are included in the HMMER3.1  src  directory  -
46       the  C  program  hmmc2  and  the perl script hmmpgmd_client_example.pl.
47       These are intended as examples only, and should be extended  as  neces‐
48       sary to meet your needs.
49
50
51       A  query  is  submitted  to  the  master from the client as a character
52       string. Queries may be the sort that would normally be handled by  phm‐
53       mer  (protein  sequence  vs  protein  database), hmmsearch (protein HMM
54       query vs protein database), or hmmscan (protein query  vs  protein  HMM
55       database).
56
57
58       The  general  form  of a client query is to start with a single line of
59       the form @[options], followed by multiple lines  of  text  representing
60       either  the  query  HMM  or fasta-formatted sequence. The final line of
61       each query is the separator //.
62
63
64
65       For example, to perform a phmmer type search of a  sequence  against  a
66       sequence  database file, the first line is of the form @--seqdb 1, then
67       the fasta-formatted  query  sequence  starting  with  the  header  line
68       >sequence-name,  followed by one or more lines of sequence, and finally
69       the closing //.
70
71
72       To perform an hmmsearch type search, the query sequence is replaced  by
73       the full text of a HMMER-format query HMM.
74
75
76       To  perform an hmmscan type search, the text matches that of the phmmer
77       type search, except that the first line changes to @--hmmdb 1.
78
79
80       In the hmmpgmd-formatted sequence database file, each sequence  can  be
81       associated  with  one or more sub-databases. The --seqdb flag indicates
82       which of these sub-databases will be queried.  The HMM database  format
83       does not support sub-databases.
84
85
86       The  result  of  each query is an undocumented data structure in binary
87       format. In the future the data will be returned in a proper  serialized
88       structure,  but  for  now,  it requires meticulous unpacking within the
89       client. The example clients show how this is done.
90
91
92
93

OPTIONS

95       -h     Help; print a brief reminder  of  command  line  usage  and  all
96              available options.
97
98
99
100

EXPERT OPTIONS

102       --master
103              Run as the master server.
104
105
106       --worker <s>
107              Run as a worker, connecting to the master server that is running
108              on IP address <s>.
109
110
111       --daemon
112              Run as a daemon using config file: /etc/hmmpgmd.conf
113
114
115       --cport <n>
116              Port to use for communication between  clients  and  the  master
117              server.  The default is 51371.
118
119
120       --wport <n>
121              Port  to  use  for  communication between workers and the master
122              server.  The default is 51372.
123
124
125       --ccncts <n>
126              Maximum number of client connections to accept. The  default  is
127              16.
128
129
130       --wcncts <n>
131              Maximum  number  of worker connections to accept. The default is
132              32.
133
134
135       --pid <f>
136              Name of file into which the process id will be written.
137
138
139       --seqdb <f>
140              Name  of  the  file  (in  hmmpgmd  format)  containing   protein
141              sequences.   The  contents  of  this  file  will  be  cached for
142              searches.
143
144
145       --hmmdb <f>
146              Name of the file containing protein HMMs. The contents  of  this
147              file will be cached for searches.
148
149
150       --cpu <n>
151              Number of parallel threads to use (for --worker ).
152
153
154

SEE ALSO

156       See  hmmer(1)  for  a master man page with a list of all the individual
157       man pages for programs in the HMMER package.
158
159
160       For complete documentation, see the user  guide  that  came  with  your
161       HMMER distribution (Userguide.pdf); or see the HMMER web page ().
162
163
164
165
167       Copyright (C) 2015 Howard Hughes Medical Institute.
168       Freely distributed under the GNU General Public License (GPLv3).
169
170       For  additional  information  on  copyright and licensing, see the file
171       called COPYRIGHT in your HMMER source distribution, or  see  the  HMMER
172       web page ().
173
174
175

AUTHOR

177       Eddy/Rivas Laboratory
178       Janelia Farm Research Campus
179       19700 Helix Drive
180       Ashburn VA 20147 USA
181       http://eddylab.org
182
183
184
185
186
187
188HMMER 3.1b2                      February 2015                      hmmpgmd(1)
Impressum