pHMMER REST

pHMMER interface: phmmer_xsede

Command line options:

input.infile_ - The main input file, containing query sequence(s) .
input.select_database_ - Enter the database file here, name will be assigned user_dataset.txt
input.custom_mxfile_ : - Obtain residue alignment probabilities from the substitution matrix in file mxfile. --mxfile custom_submatrix.txt"

User Configurable Parameters.

vparam.runtime_ - (Float) Maximum Hours to Run (up to 168 hours)
vparam.num_cores_ - (Integer) How many cores do you need? Default = 2
vparam.seed_val_ - (lnteger)  Enter the seed value here --seed default = 42

Options Controlling Scoring System
vparam.set_gapvalue_ - (Float) Gap open probability for a single sequence query model (--popen) vdef = 0.02, between 0 and 0.5
vparam.set_gapextendvalue_ - (Float) Gap extend probability for a single sequence query model (--pextend), default = 0.4, between 0 and 1.
vparam.specify_alignprobs_ - (Excl) Obtain residue alignment probabilities from specified substitution matrix (--mx) PAM30, PAM70, PAM120, PAM240, BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80

Options Controlling Reporting Thresholds

vparam.set_evalue_ - (Float)  Report target sequences with an E-value of (-E); default = 10.0
vparam.specify_bitscore_ - (Float) Report target sequences with a bit score of (-T); instead of -E
vparam.specify_domevalue_ - (Float) Conditional E-value for individual domains (--domE) default=10.0
vparam.specify_dombitscore_ - (Float) Report domains with bit score value of (--domT) instead of domE.

Options Controlling Output
vparam.output_file_ - (String) Write output to this file (-o)
vparam.multialignment_file_ - (Switch) Save a multiple alignment of all significant hits (-A) default=0.
vparam.tblout_file_ - (String)  Save simple tabular file summarizing per-target output (-tblout)
vaparam.domtblout_file_ - (String) Save a simple tabular file summarizing the per-domain output (-domtblout)
vparam.pfamtblout_file_ - (String) Save tabular file summarizing the per-target output (-pfamtblout)
vparam.use_accessions_ (Switch) Use accessions instead of names in the main output (--acc)
vparam.omit_alignment_ - (Switch) Omit the alignment section from the main output. (--noali)
vparam.unlimit_length_ (Switch)  Unlimit the length of each line in the main output (--notextw)
vparam.setlimit_length_ (Integer)Limit the main output’s line length (--textw)

Options Controlling H3 Parameter Estimation

vparam.specify_seqlength_ - (Integer) Specify the sequence length in simulation (--EmL) default=200
vparam.specify_seqnum_ - (Integer) Sets the number of sequences to estimate mu for MSV (--EmN) default =200
vparam.specify_seqlength2_ - (Integer) Length of sequence to estimate mu for Viterbi (--EvL) default=200
vparam.specify_seqnum2_ - (Integer) Number of sequences to estimate mu for Viterbi (--EvN) default=200
vparam.specify_seqlength3_ - (Integer) Sequence length to estimate tau (--EfL) default=100
vparam.specify_seqnum3_ - (Integer) Sequence number to estimate tau (--EfN) default=200
vparam.specify_tailmassfr_ - (Float) Sets the tail mass fraction (--Eft)0.04

Options Controlling the Acceleration Pipeline

vparam.disable_filters_ - (Switch) Turn off all filters (--max) default=0
vparam.specify_pvalue_ - (Float) vparam.specify_pvalue2_ - (Float) Set the P-value threshold for the Viterbi filter step (--F2) default= 0.001
vparam.specify_pvalue3_ - (Float) Set the P-value threshold for the Forward filter step (--F3) default=0.00001

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