TransMem+

P Plus programs are enhanced to be able to read sequences in a variety of native formats such as GCG RSF, GCG SSF, GCG MSF, GenBank, EMBL, FastA, SwissProt, PIR, and BSML without conversion.

P Plus programs remove sequence length restriction of 350,000bp.

If you do not need these features and wish to have more interactivity, you might wish to seek out and run the original program version.

TransMem+ builds on the method of Sonnhammer et al. (Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, 175-182 (1998)) to predict likely transmembrane helices in one or more input proteins. The method is based upon a Hidden Markov Model (HMM) that has been trained on a set of membrane proteins with helical membrane spanning regions.

EXAMPLE

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Here is a session using TransMem+ to generate predictions for the 17Kda Surface antigens of Rickettsia.

20:16~74> transmem+

Transmem+ is a program that finds the Trans membrane regions for a given protein sequence. It is based upon Hidden Markov Model (HMM) architecture. The architecture is made up of 7 types of states corresponding to the core of the transmembrane helix, helix caps, cytoplasmic loops, short and long cytoplasmic loop states, and globular domains that are part of each loop.

transmem+ of which protein sequence(s) ? uniprot:17kd*

What should I call the output file (* <sequence_name>.transmem+ *) ?

Analyzing sequence '17KD_RICAM' from 'uniprot_sprot:17KD_RICAM'

Processing results...

No helices were found in uniprot_sprot:17KD_RICAM

Analyzing sequence '17KD_RICAU' from 'uniprot_sprot:17KD_RICAU'

Processing results...

No helices were found in uniprot_sprot:17KD_RICAU

Analyzing sequence '17KD_RICCA' from 'uniprot_sprot:17KD_RICCA'

Processing results...

Analyzing sequence '17KD_RICCN' from 'uniprot_sprot:17KD_RICCN'

Processing results...

No helices were found in uniprot_sprot:17KD_RICCN

Analyzing sequence '17KD_RICJA' from 'uniprot_sprot:17KD_RICJA'

Processing results...

No helices were found in uniprot_sprot:17KD_RICJA

Analyzing sequence '17KD_RICMO' from 'uniprot_sprot:17KD_RICMO'

Processing results...

No helices were found in uniprot_sprot:17KD_RICMO

Analyzing sequence '17KD_RICPA' from 'uniprot_sprot:17KD_RICPA'

Processing results...

No helices were found in uniprot_sprot:17KD_RICPA

Analyzing sequence '17KD_RICPR' from 'uniprot_sprot:17KD_RICPR'

Processing results...

No helices were found in uniprot_sprot:17KD_RICPR

Analyzing sequence '17KD_RICRH' from 'uniprot_sprot:17KD_RICRH'

Processing results...

No helices were found in uniprot_sprot:17KD_RICRH

Analyzing sequence '17KD_RICTY' from 'uniprot_sprot:17KD_RICTY'

Processing results...

No helices were found in uniprot_sprot:17KD_RICTY

Results written to transmem+.out

OUTPUT

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The output from TransMem+ is a list file, and is suitable for input to any GCG program that allows indirect file specifications. (For information about indirect file specification, see Section 2, Using Sequence Files and Databases of the User's Guide.)

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICAM !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICAM

P50927 rickettsia amblyommii. 17 kda surface antigen precursor (fragment). 10/2003

Begin End

Outside 1 154

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALAASTLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGKG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ VGAGMDEQDR RIAELTSQKA LETAPNGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYVTPNKTYR NSTGQYCREY TQTVVIGGKQ QKAYGNACRQ

OOOO

151 PDGQ

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICAU !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICAU

P50928 rickettsia australis. 17 kda surface antigen precursor (fragment). 10/2003

Begin End

Outside 1 154

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALAASMLQAC NSPGGMNKQG TGTLLGGAGG ALLGSQFGKG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGAGMDEQDR RLAELTSQRA LETAPSGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYVTPNKTYR NSNGQYCREY TQTVVIGGKQ QKAYGNACRQ

OOOO

151 PDGQ

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICCA !1 1 1

\\End of List

>>uniprot_sprot:17KD_RICCA

P29697 rickettsia canada. 17 kda surface antigen (fragment). 10/1996

Begin End

Outside 1 11

Helix 12 30

Inside 31 80

OOOOOOOOOO OHHHHHHHHH HHHHHHHHHH IIIIIIIIII IIIIIIIIII

1 GSQFGKGKGQ LIGVGAGALL GAILGNQIGA GMDEQDRRLA ELTSQRALET

IIIIIIIIII IIIIIIIIII IIIIIIIIII

51 TPSGTSIEWR NPDNGNYGYV TPSKTYKNST

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICCN !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICCN

P05372 rickettsia conorii, and rickettsia rickettsii. 17 kda surface antigen precursor. 10/2003

Begin End

Outside 1 159

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALATSMLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGKG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGAGMDEQDR RLAELTSQRA LETAPSGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYVTPNKTYR NSTGQYCREY TQTVVIGGKQ QKAYGNACRQ

OOOOOOOOO

151 PDGQWQVVN

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICJA !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICJA

Q52764 rickettsia japonica. 17 kda surface antigen precursor. 10/2003

Begin End

Outside 1 159

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALATSMLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGKG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 TGQLVGVGVG ALLGAVLGGQ IGAGMDEQDR RLAELTSQRA LETAPSGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYVTPNKTYR NSTGQYCREY TQTVVIGGKQ QKAYGNACRQ

OOOOOOOOO

151 PDGQWQVVN

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICMO !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICMO

P50929 rickettsia montana. 17 kda surface antigen precursor (fragment). 10/2003

Begin End

Outside 1 154

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALAASMLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGQG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGAGMDEQDR RLAELTSQRA LETAPSGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYVTPNKTYR NSTGQYCREY TQTVVIGGKQ QKAYGNACLQ

OOOO

151 PDGQ

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICPA !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICPA

P50930 rickettsia parkeri. 17 kda surface antigen precursor (fragment). 10/2003

Begin End

Outside 1 154

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMVI ALATSMLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGKG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGAGMDEQDR RLAELTSQRA LETAPSGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYVTPNKTYR NSTGQYCREY TQTVVIGGKQ QKAYGNACLQ

OOOO

151 PDGQ

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICPR !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICPR

P16624 rickettsia prowazekii. 17 kda surface antigen precursor. 10/2003

Begin End

Outside 1 159

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALAASMLQAC NGQSGMNKQG TGTLLGGAGG ALLGSQFGQG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGASMDEQDR RLLELTSQRA LESAPSGSNI

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNH GYVTPNKTYR NSAGQYCREY TQTVIIGGKQ QKTYGNACRQ

OOOOOOOOO

151 PDGQWQVVN

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICRH !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICRH

P50931 rickettsia rhipicephali. 17 kda surface antigen precursor (fragment). 10/2003

Begin End

Outside 1 154

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKIMII ALAASMLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGKG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGAGMDEQDR RLAELTSQRA LETAPSGSNV

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNY GYITPNKTYR NSTGQYCREY TQTVVIGGKQ QKAYGNACLQ

OOOO

151 PDGQ

Sequences examined:1

Sequences written:1

!!SEQUENCE_LIST 1.0

Transmem of uniprot:17kd*

-MINHelix = 0

-MEthod = VITERBI

-nbest = 1

-PROXimity = 0

Tue Dec 7 20:16:21 2004

Helix Inside Outside

uniprot_sprot:17KD_RICTY !0 0 1

\\End of List

>>uniprot_sprot:17KD_RICTY

P22882 rickettsia typhi. 17 kda surface antigen precursor. 10/2003

Begin End

Outside 1 159

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

1 MKLLSKVMIL ALAASMLQAC NGPGGMNKQG TGTLLGGAGG ALLGSQFGHG

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

51 KGQLVGVGVG ALLGAVLGGQ IGASLDEQDR KLLELTSQRA LESAPSGSNI

OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO OOOOOOOOOO

101 EWRNPDNGNH GYVTPNKTYR NSTGQYCREY TQTVVIGGKQ QTTYGNACRQ

OOOOOOOOO

151 PDGQWQVVN

Sequences examined:1

Sequences written:1

INTERPRETING OUTPUT

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The first part of the output file contains a list of all the sequences searched and the predictions generated for a given sequence. When multiple predictions are generated for each sequence, the predictions are listed in order of prediction quality, with the best prediction on top and the sub-optimal predictions below.

Next to each sequence, the file contains the raw counts of how many transmembrane helices, inner loops, and outer loops were found. If you have generated more than one prediction per sequence, there is also a score reported for comparing the quality of the prediction with the best prediction for each sequence. This is a relative measure only and should not be used to compare the quality of predictions between different sequences. In general, a score of 10 or more indicates that the prediction is significantly different from the best prediction.

Following this list of sequences, TransMem+ displays a table listing the specific boundaries of each feature predicted, followed by the sequence aligned with the predicted labels.

INPUT FILES

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TransMem+ takes any valid GCG specification for one or more protein sequences.

RELATED PROGRAMS

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SPScan+ scans protein sequences for the presence of secretor signal peptides (SPs).

HTHScan+ scans protein sequences for the presence of helix-turn-helix motifs, indicative of sequence-specific DNA-binding structures often associated with gene regulation.

SPScan scans protein sequences for the presence of secretor signal peptides (SPs).

HTHScan scans protein sequences for the presence of helix-turn-helix motifs, indicative of sequence-specific DNA-binding structures often associated with gene regulation.

HelicalWheel plots a peptide sequence as a helical wheel to help you recognize amphiphilic regions.

PeptideStructure makes secondary structure predictions for a peptide sequence. The predictions include (in addition to alpha, beta, coil, and turn) measures for antigenicity, flexibility, hydrophobicity, and surface probability. PlotStructure displays the predictions graphically.

PepPlot plots measures of protein secondary structure and hydrophobicity in parallel panels of the same plot.

CoilScan+ locates coiled-coil segments in protein sequences.

CoilScan locates coiled-coil segments in protein sequences.

TransMem scans for likely transmembrane helices in one or more input protein sequences.

RESTRICTIONS

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TransMem+ only works on protein sequences.

ALGORITHM

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TransMem+ is based upon Hidden Markov Model (HMM) architecture. The architecture is made up of 7 types of states corresponding to the core of the transmembrane helix, helix caps, cytoplasmic loops, short and long cytoplasmic loop states, and globular domains that are part of each loop.

The states have a close relationship with the biology of membrane proteins; loop states connection to other loops through a helix cap, helix core, and another helix cap. These states correspond to one of three different labels, Inside (cytoplasmic), Helix (membrane spanning helix), and Outside (non-cytoplasmic).

The prediction of transmembrane helices is done by finding an optimal alignment of the sequence with the model using the N-Best algorithm. In the N-Best algorithm, the algorithm uses the model architecture to find the best labeling of the sequence, given the model.

Alternatively, you can run TransMem+ using the Viterbi algorithm, which finds the optimal alignment of the sequence with the model, then uses that alignment to read the labels. In general, the Viterbi algorithm will give the same results as the N-Best, but in some cases the predictions will differ.

The output of the raw probabilities is based upon the forward-backward algorithm, in which TransMem+ finds the probability of each labeling (Inside, Outside, or Helix) summed over all the possible alignments of the sequence to the model. Because these values are based upon all possible alignments of the model instead of a single optimal alignment, occasionally the raw probabilities will contradict the final labeling.

CONSIDERATIONS

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When no transmembrane helices are predicted, it is not a good idea to treat the Inside/Outside prediction as an accurate measure of whether or not the peptide is secreted. The inner and outer labeling is only meaningful for integral membrane proteins.

When using the N-Best algorithm, you can also choose to merge predictions with a given overlap. The boundaries of transmembrane helices have an experimental error of a few residues, a fact which was incorporated into the training of the model architecture. By allowing a merging of overlapping predictions, TransMem+ allows you to blur edges of the predicted helices, which in turn will cause the N-Best algorithm to generate predictions with significant differences.

The N-Best algorithm will always try to find the best labeling of your sequence that matches the parameters of minimum and maximum number of helices, even if this is not the best overall labeling. For example, if you have some other experimental evidence that suggests you are working with a 7 transmembrane protein, yet the algorithm gives you a prediction of 8 transmembrane helices, you can specify a minimum and maximum helix range of 7, which will force the algorithm to find this prediction. If the application is not able to find any matching predictions, try increasing the value of N-Best, which will increase the number of different predictions that the algorithm will consider.

By increasing the number of different predictions generated, you are increasing the number of different predictions that TransMem+ analyzes. Consequently, you may see weakly predicted helices that would otherwise not be visible, as well as many more false predictions. Additionally, if a helix is visible in a large number of predictions, it is more likely to be an actual helix and not a false positive. Since you are increasing the number of predictions considered, computation time will also increase dramatically with increases in the value for N-Best.

Because of the N-Best algorithm's ability to try to find a prediction that matches the restrictions; it may not be useful for screening protein sequences for a given number of transmembrane helices. Instead, we recommend using the Viterbi algorithm, which is more discriminating and runs faster.

If you have a sequence for which you have experimental evidence of a particular number of transmembrane helices, yet the algorithm does not predict the correct number, specify this number with -MINHelix and -MAXHelix, then try increasing the value for N-Best and the tolerance for merging overlapping predictions. In some cases, this will allow the algorithm to find the helices.

If you are screening large amounts of data for 7 transmembrane proteins, for example, it probably isn't a good idea to limit the search for predictions of only 7 transmembrane regions. Instead, more complete searches can be generated from searching for anything containing 6-8 transmembrane regions.

TransMem+ only recognizes transmembrane alpha helices. All other types of membrane spanning regions are not recognized.

A Since TransMem+ will produce a self-consistent topology prediction, if it misses any transmembrane helices, the topology will be wrong.

Predicted transmembrane helices in the n-terminal region sometimes turn out to be signal peptides.

SCIENTIFIC VALIDITY

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A non-redundant data set of 148 sequences, composed of all known transmembrane proteins (Möller et al, 2001), was used for validation of this program. The data set was run through the public server and through this implementation.

All except 8 sequences showed identical results (95% identical). NB: When the predictions differed, this program found the other prediction as the second best answer.

Of these 8 differences, 4 (COX2_BOVIN, IMMA_CITFR, RCEL_RHOVI, and TCR2_ECOLI) only differed in the exact positions of the helix boundaries. All predicted helices from the two implementations overlapped by at least 16 residues, and the topology predictions were identical.

There were 2 of the 8 proteins (COXH_BOVIN and CYB_RHOSH) where the topology predictions of the two implementations were reversed in addition to minor helix boundary differences. This implementation was correct for COXH_BOVIN and the public server was correct for CYB_RHOSH.

In the final 2 sequences, (CITN_KLEPN and CYOB_ECOLI), the two predictions differed in the presence or absence of a given TM helix. This implementation correctly found an additional helix in CITN_KLEPN. For CYOB_ECOLI, the public server correctly found an additional TM helix that this implementation did not find.

In conclusion, the two implementations are scientifically comparable. Half of the differences could be attributed to minor variation in TM helix boundaries, which are not significant differences, due to the inherent uncertainty in experimental determination of the helix boundaries. When the different implementations gave significant differences, there was an even split between which answer was correct.

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 syntax summary below, square brackets ([ and ]) enclose parameter values that are optional. For each program parameter, square brackets enclose the type of parameter value specified, the default parameter value, and shortened forms of the parameter name, aliases. Programs with a plus in the name use either the full parameter name or a specified alias. If “Type” is “Boolean”, then the presence of the parameter on the command line indicates a true condition. A false condition needs to be stated as, parameter=false.

20:16~75> transmem+ -che

Transmem+ is a program that performs an HMM search of any number of sequences against an HMM.

Minimal Syntax: % transmem+ [-infile=]value -Default

Minimal Parameters (case-insensitive):

-infile         [Type: InFile / Default: EMPTY / Aliases: infile1 in]

                The name of the input file.

Prompted Parameters (case-insensitive):

-outfile        [Type: OutFile / Default: '<sequence_name>.transmem+' /

                Aliases: out] Names the output file.

Optional Parameters (case-insensitive):

-check          [Type: Boolean / Default: 'false' / Aliases: che help]

                Prints out this usage message.

-default        [Type: Boolean / Default: 'false' / Aliases: d def]

                Specifies that sensible default values be used for all parameters where possible.

-documentation  [Type: Boolean / Default: 'true' / Aliases: doc]

                Prints banner at program startup.

-quiet          [Type: Boolean / Default: 'false' / Aliases: qui]

                Tells application to print only a minimal amount of information.

-seqout         [Type: OutFile / Default: EMPTY / Aliases: rsf]

                Annotated sequence output.

-method         [Type: String / Default: 'VITERBI' / Aliases: me] Selects which method to use to generate the prediction. Valid values are VITERBI and NBEST.

-architecture   [Type: InFile / Default: '$GCGROOT/share/hmm/tmhmm.arch' / Aliases: arch] Sets the HMM architecture file.

-nbest          [Type: Integer / Default: '1' / Aliases: nb] Number of different annotations of each sequence. Only applies when method=NBEST.

-proximity      [Type: Integer / Default: '0' / Aliases: prox] Proximity of feature boundaries to consider annotations                equivalent. Only applies when method=NBEST.

-rawprob        [Type: Boolean / Default: 'N' / Aliases: raw] Writes out the raw probabilities of each label for each sequence character.

-maxhelix       [Type: Integer / Default: '2147483647' / Aliases: maxh] Only show proteins with at most this many transmembrane helices (default is unlimited).

-minhelix       [Type: Integer / Default: '0' / Aliases: minh] Viterbi algorithm:Only show proteins with at least this many transmembrane helices.NBest algorithm : Forces the algorithm to find at least this many helices.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line. Shortened forms of the parameter name, aliases, are shown, separated by commas.

-nbest, -nb

Specify how many predictions you want to see. The most likely predictions are the first one listed. Note that larger numbers of predictions can greatly reduce program speed.

      -infile, -infile1, -in

                     The name of the input file.

      -outfile, -out

                       Names the output file.

-check, -che, -help

Prints out this usage message.

-default, -def

Specifies that sensible default values be used for all parameters where possible.

-documentation, -doc

Prints banner at program startup.

-quiet, -qui

This parameter is not supported.

-seqout

Annotated sequence output.

-method, -me

Selects which method to use to generate the prediction. Valid values are VITERBI and NBEST.

-architecture, -arch

Sets the HMM architecture file.

-proximity, -prox

Proximity of feature boundaries to consider annotations equivalent. Only applies when method=NBEST.

-rawprob, -rawp

Output the raw probabilities for observing each label at each sequence character. These values are based upon the forward-backward algorithm and may not agree with the final predicted label.

-maxhelix, -maxh

Limit the output to include only proteins with this many transmembrane helices or fewer. By default, the maximum number of helices is unlimited.

-minhelix, -minh

Limit the output to include only proteins with this many or more transmembrane helices. If this value is greater than specified with -maxhelix, the value for maxhelix is used. By default, the output only includes proteins with one or more helix.

Printed: May 27, 2005 14:58

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