HMMEREMIT

Table of Contents

FUNCTION

DESCRIPTION

EXAMPLE

FUNCTION

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HmmerEmit generates sequences that match a profile hidden Markov model.

DESCRIPTION

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HmmerEmit provides a Accelrys GCG (GCG) interface to the hmmemit program of Dr. Sean Eddy's HMMER package. It allows you to access most of hmmemit's parameters from GCG command line.

HmmerEmit randomly generates sequences that match a given profile HMM. These are output in a single RSF file, and can be output as is, or with gaps inserted as necessary so that they are in alignment with each other. It can also create a single majority-rule consensus sequence for the profile HMM.

EXAMPLE

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Here is a session using HmmerEmit to generate a set of sequences from the HMM created in the HmmerBuild session:

% hmmeremit

HMMEREMIT sequences representative of what profile HMM ? hsp70.hmm_g

What should the output file be called (* hmmeremit.rsf *)?

Creating temp file for input to hmmemit.

Calling hmmemit to perform analysis ...

hmmemit - generate sequences from a profile HMM

HMMER 2.1.1 (Dec 1998)

HMMER is freely distributed under the GNU General Public License (GPL).

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HMM file: /usr/users/share/smith/hsp70.hmm_g

Number of seqs: 10

Random seed: 966634453

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

OUTPUT

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Here is some of the output file:

!!RICH_SEQUENCE 1.0

Output generated by GCG HMMER

..

name  seq1

type    PROTEIN

checksum    8442

creation-date  9/13/1999 17: 5:55

strand  1

sequence

  SDYNSISSNGIGIDLGTTTSVVASMPDDRIQIIANDSGNRFTPNGVAFTEKETLIGMYSK

  DQSACMSKNTLFDAKRLIARKFNDDRVQPDSKCWPLVVIGRVKKPQIQVKVLGFAKEFAP

  PEMSSMIVTKMKEQAESFLNEVVGAALITIPAYFNDSQRTATIDAGTIAGLNVLRLVAEP

  TAAAAAYRLDKATRIKERNYLIFDLGGGTHDIELMTINRDGTFEVRSTSFDVHLGGEDFD

  RRLLPALCYEFKRKKADKDLETDTAAMKRLAYAAETAKVELSSSTSVCIELDALFKGGQG

  YKKVYPRVCRAKFESLNQDLFQRTLDPMEKALRDAEVDKAQVAKLVLVGGSTRLPMVLRL

  VNEFFNGKEQRKVINSDEAVSLPAAVQGGLLEGLAGDKDFLLLDVDPVAMGMMIQGGVMN

  ALEKRNSVVPCKKAQVFTTTSGNRTSMLVEASDGERDSCANELLGRFTLKGIMPAPAGVP

  QFVPQFDVEALGILYVSSKKKNAGKINKKTIANIKALSTVKIEKMIEEAIRYKTADEKNS

  KRIVGAEHLEHYAYNLKQTIKDMKEKLTENDYSIVESQIERIETLLDRNNDSIFKLKAQM

  DEAVIMPVIKLYKFRTLDAANSKDNQLDGSSARAGTVWNASSPDSNECLNPGGDKSGPMI

  EDID

name  seq2

type    PROTEIN

checksum    5720

creation-date  9/13/1999 17: 5:55

strand  1

sequence

  GTSGEKVGIDLLTTSSMKHSNSAVSKYVPRRVEMLENAQGNRSTPSLLIYTDEEALGDRI

  SIGAAAKNQVALNDSNTVFAAGRLMGRKFSDLSVQRDLKFFPANMQPDQQEGVKANIEVP

  FKEEPGKFGPKEISGEILSAMNEVAETYWGKEHVVGEAVVTVPTYVGDAQKQVGKDAGRL

  AELNVDRLIEEPTACCLAYGLDKSKKQPLHFDLGGGAFDVTLLHLDVNVFEVKATSGQTE

  LGATGFDNEMIPSHVHYVKRKNAHIDTGDNERSLQRIRTEDDQAKRDLASPGQTSIRVES

  VTEGVAFHSEFSIKITRAKYETLFLNSIAPVEQPPLRIASMSKQQMDEVMLVGGSTGIPK

  VQEDIVQYFSGKDPHKMIIPDEAVAYGAAIQAYILKGEEISRTKDILLDDIAPKSIGIST

  RQGVMTYYIAANLCISTEKSSLFSTVADNQPSVQNVSQDGEMQMVKDNHSLGTFGIGGIN

  PAGAMIEVTFGIQANPVLDMAYNDTNTGSTGNITIDNDRGSMSEMEIDDMVEEAVEFADD

  QEEARHQTAKTRLTEKYAQQTGTGVVENSKERMSGTDKKKIEDNIEGVTNALQVNDTPTQ

  KEEFRDAHATLENSVTKAFEKMHQGARSGKTISRAASYNDKRVVGVTEEINAVEWNAPNI

  TPIRSGGQGESVE

//////////////////////////////////////////////////////////////

name  seq10

type    PROTEIN

checksum    1351

creation-date  9/13/1999 17: 5:55

strand  1

sequence

  EEKAIGIQLGVAYACMGAYKAGTVVILPENHQGNRITPSYIAFTDDELLVGAAAKTQVAS

  NPQNTHFDARQLIGRKFKDKEVQAEIHHLQFKINSAGREEAKSNYQYKGSLFSAEQLSSL

  VVAKMKENAHAYLGKTVIQAVRTVPAYFNDLQRQTKYDAGLIAALNVLRFINEPTMAIAY

  GTDKVGGQSEETVILIYDDGEGKMEVSIKGSYENKAQGETHLGGDNYSDEMDQVLKQEFP

  TKNKGDDINSNAYASRRLRDAAERSERQLSSAPMNLIEIASFDDEADGPRLDTEGSRGTR

  AKLETLNRELFAGTLSPVNRALRDAKLDKAQITDVVKVGGSLRIAKVIKCVKDFSNGREF

  NKSINPEENVALGAPVQGAVKGQTVANNVADILLLDVTPLSLGLRTEGDVMTVMIFKNTT

  VPTKKDWTFSTYVRNQGMVYLKVFEGERTAQDQDLLGRWELCGIPPEKLKPRGFPQFEVR

  FDFAANGILDVKAGEKGTNKANRITITMYKGACKKKEIQKEVAEADSFQEGDSKENQLKG

  ATNNAESLSDYNLRNTCKDTAISTGVTEAKKTEAITDRCQPFLALVTELALREQYDTAFR

  ELEGVCKPSVFNRYCFHQQGTEAGRPKSHCTGSEKMEVPCDEKGPGLMSQKLRVKGTSSN

  PSTREVD

INPUT FILES

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HmmerEmit requires as its only input a profile HMM file.

RELATED PROGRAMS

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PileUp creates a multiple sequence alignment from a group of related sequences. Pretty displays multiple sequence alignments.

ProfileMake makes a profile from a multiple sequence alignment. ProfileSearch uses the profile to search a database for sequences with similarity to the group of aligned sequences. ProfileSegments displays optimal alignments between each sequence in the ProfileSearch output list and the group of aligned sequences (represented by the profile consensus). ProfileGap makes optimal alignments between one or more sequences and a group of aligned sequences represented as a profile. ProfileScan finds structural and sequence motifs in protein sequences, using predetermined parameters to determine significance.

HmmerBuild makes a profile hidden Markov model from a multiple sequence alignment. HmmerAlign aligns one or more sequences to a profile HMM. HmmerPfam searches a database of profile HMMs with a sequence query in order to identify known domains within the sequence. HmmerSearch uses a profile HMM as a query to search a sequence database for sequences similar to the original aligned sequences. HmmerCalibrate calibrates a hidden Markov model so that database searches using it as a query will be more sensitive. HmmerIndex creates a binary GSI ("generic sequence index") for a database of profile HMMs. HmmerFetch retrieves a profile hidden Markov model by name from an indexed database of profile HMMs. HmmerEmit randomly generates sequences that match a profile HMM. HmmerConvert converts between different profile HMM file formats and from profile HMM to GCG profile file format.

MEME finds conserved motifs in a group of unaligned sequences and saves these motifs as a set of profiles. You can search a database of sequences with these profiles using the MotifSearch program.

RESTRICTIONS

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Unknown.

ALGORITHM

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See the Profile HMM Analysis Essay for an introduction to profile hidden Markov models and the terminology associated with them.

To generate sequences that match the model, HmmerEmit uses a random number generator that is initialized by a seed value. By default, this seed value is derived from the system clock of your computer, so each program run will use a different seed and thus generate a somewhat different set of sequences. If you want HmmerEmit to generate the same set of sequences each time, you can set the seed by means of the -SEED parameter.

When generating a single consensus sequence, HmmerEmit looks at the state probabilities at each node of the model. If the probability of a match state at a node is greater than or equal to 0.5, the most likely residue at that node (the one with the highest emission probability) is written to the consensus sequence. On the other hand, if the probability of an insert state at that node is greater than or equal to 0.5, one or moreX characters are written to the consensus, the number of characters depending on the expectation value of the insert state at that node.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional.

Minimal Syntax: % hmmeremit [-INfile1=]hsp70.hmm_g -Default

Prompted Parameters:

[-OUTfile=]hsp70.rsf names the output file

Local Data Files: None

Optional Parameters:

-MULTIAlign writes the generated sequences so that they are in alignment

-CONsensus creates a single majority-rule consensus sequence

-SEQNUM=10 generates 10 sequences that match the model

-SEED=13794 sets the seed for the random number generator to 13794

-NOMONitor doesn't display information about analysis parameters used

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line.

Following some of the parameters described below is a short expression in parentheses. These are the names of the corresponding parameters used in the native HMMER package. Some of the GCG parameters are identical to the original HMMER parameters, others have been changed to fit GCG's conventions.

-MULTIAlign (-a)

Writes the generated sequences to the RSF file so that they are in alignment with each other. (Gaps are inserted into the sequences as needed in order to accomplish this.) This option can not be used together with parameter -CONsensus.

-CONsensus (-c)

Creates a single majority-rule consensus sequence. Highly conserved residues (probability greater than or equal to 90 percent for DNA and greater than or equal to 50 percent for protein) are shown in uppercase; less conserved residues are shown in lowercase. If insert states are used in more than 50 percent of generated sequences, they may become part of the majority rule consensus. If so, the insert-generated residues are shown as X. This option can not be used together with parameter -MULTIAlign. Also if this option is used, parameter -SEQNUM will always be ignored.

-SEQNUM=10 (-n 10)

Generates 10 sequences (10 is the default). This option will be ignored if parameter -CONsensus is specified as well.

-SEED=13794 (--seed 13794)

Sets the seed for the random number generator to 13794 (must be a positive integer) instead of using the system clock to create the seed.

-NOMONitor

Suppresses the display of the program's progress on the screen.

Printed: May 27, 2005 12:43

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