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HMMER(1)			 HMMER Manual			      HMMER(1)

       HMMER - profile HMMs for	biological sequence analysis

	 Align sequences to a profile

	 Construct profiles from multiple sequence alignments

	 Convert profile file to various formats

	 Sample	sequences from a profile

	 Retrieve profiles from	a file

	 Produce a conservation	logo graphic from a profile

	 Daemon	for database search web	services

	 Prepare a profile database for	hmmscan

	 Search	sequence(s) against a profile database

	 Search	profile(s) against a sequence database

	 Collect profile score distributions on	random sequences

	 Summary statistics for	a profile file

	 Iteratively search sequence(s)	against	a sequence database

	 build nhmmer database from a sequence file

	 Search	DNA/RNA	queries	against	a DNA/RNA sequence database

	 Search	DNA/RNA	sequence(s) against a DNA/RNA profile database

	 Search	protein	sequence(s) against a protein sequence database

	 Calculate and add column mask to a multiple sequence alignment

       HMMER  is a suite of several programs for biological sequence alignment
       and database homology search. It	uses probabilistic models called "pro-
       file  hidden Markov models" (profile HMMs) to represent the likely evo-
       lutionary homologs of a single sequence or a multiple  alignment	 of  a
       sequence	family.	A main avenue of research is to	improve	the evolution-
       ary predictive models in	HMMER to be able to recognize  and  accurately
       align increasingly remote homologs, distant in time.

       HMMER  is  also	used  as an organizational tool, to group the exponen-
       tially growing number of	biological sequences into a vastly smaller set
       of  well-annotated sequence families. New sequences can be annotated by
       comparison against curated sequence family databases of prebuilt	 HMMER
       profiles,  in  addition or instead of comparison	to the entire sequence
       database. Databases such	as Pfam, SMART,	and  TIGRfams,	among  others,
       are based on this principle.

       HMMER  is  used	in three main modes: to	search a sequence database for
       new homologs of a sequence or a sequence	family;	to  search  a  profile
       database	(like Pfam) to find what known family a	query sequence belongs
       to, or what domains it has; and to automatically	construct large	multi-
       ple alignments (i.e. with an effectively	unlimited number of sequences)
       using a profile representative of a sequence family.

       Suppose you have	a multiple sequence alignment of a sequence family  of
       interest, and you want to search	a sequence database for	additional ho-
       mologs. The hmmbuild program builds  profile(s)	from  multiple	align-
       ment(s).	  The  hmmsearch program searches protein profile(s) against a
       protein sequence	database, and nhmmer  searches	nucleotide  profile(s)
       against a nucleotide sequence database.

       Suppose	you have a single sequence of interest,	and you	want to	search
       a  sequence  database  for  additional  homologs.  The  phmmer  program
       searches	a single protein sequence against a protein sequence database.
       The jackhmmer program does the same thing but iteratively  --  homologs
       detected	 in  a previous	round are incorporated into a new profile, and
       the new profile is searched again.  phmmer is  used  like  BLASTP,  and
       jackhmmer is used like a	protein	PSI-BLAST. The nhmmer program searches
       a single	nucleotide sequence against a nucleotide sequence.

       Suppose you have	sequence(s) that you want to analyze  using  a	HMMER-
       based  profile  HMM database like Pfam (  The
       hmmpress	program	formats	a profile HMM flatfile (such as	the  file  you
       would  download	from  Pfam) into a HMMER binary	database.  The hmmscan
       program searches	protein	sequence(s) against that database.  The	 nhmm-
       scan  program  can  similarly  search  nucleotide sequence(s) against a
       pressed	database  of  nucleotide   profiles,   such   as   from	  Dfam

       Suppose	you  want to align lots	of sequences. You can construct	a man-
       ageably small alignment of a representative set of sequences,  build  a
       profile with hmmbuild, and use the hmmalign program to align any	number
       of sequences to that profile.

       HMMER also includes some	auxiliary tools	for working with large profile
       databases.   hmmfetch  fetches  one  or	more profiles from a database.
       hmmstat prints summary statistics about a profile file.

       For compatibility with other profile software and previous versions  of
       HMMER, the hmmconvert program converts profiles to a few	other formats.
       We intend to add	more support for other formats over time.

       The hmmemit program generates  (simulates)  "homologous"	 sequences  by
       sampling	from a profile.	It can also generate a "consensus" sequence.

       The  hmmsim program is a	simulator used for collecting statistics about
       score distributions on random sequences.

       Each program has	its own	man page.

       This is a summary man page for the entire HMMER3	package.  See individ-
       ual  man	 pages	[hmmbuild(1), for example] for usage, options, and de-
       scription of each program in the	package.

       For complete documentation, see the user	guide that came	with your  HM-
       MER distribution	(Userguide.pdf); or see	the HMMER web page (http://hm-

       Copyright (C) 2019 Howard Hughes	Medical	Institute.
       Freely distributed under	the BSD	open source license.

       For additional information on copyright and  licensing,	see  the  file
       called  COPYRIGHT  in  your HMMER source	distribution, or see the HMMER
       web page	(


HMMER 3.3			   Nov 2019			      HMMER(1)


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