5 File types

: 6 Parameter specification : SAM (Sequence Alignment and : 参考文献 目次

#
5 File types

SAM produces a variety of files. This section summarizes both the extensions SAM uses and the extensions we conventionally use when naming output that goes to standard output.

The following file extensions are automatically used:

.a2m
  A SAM alignment file, as created by `align2model` or `hmmscore`. A FASTA-compatible format. See Section 10.1.
.apr
  A SAM alignment probabilities file, as created by `pathprobs`. An RDB-compatible format. See Section 10.8.
.ckp
  A PSI-BLAST checkpoint profile file created by `sam2psi`, which can be used with PSI-BLAST in conjunction with the matching `.cks` checkpoint sequence file. See Section 10.10.6.
.cks
  A PSI-BLAST checkpoint sequence file created by `sam2psi`, which can be used with PSI-BLAST in conjunction with the matching `.ckp` checkpoint profile file. See Section 10.10.6.
.cst
  A SAM constraints file containing the definition of sequence position constraints. See Section 9.7.
.data
  A `gnuplot` data file generated by `makehist`. See Section 10.11.
.dist
  A scoring file listing sequence identifiers, lengths, and scores, produced by `hmmscore`. See Section 10.2.
.dist-rdb
  A scoring file in RDB format including sequence identifiers, lengths, scores, and information about scoring method produced by `hmmscore`. See Section 10.2.
.frag
  An a2m alignment file generated by `fragfinder`. See Section 10.4.
.freq
  A frequency model generated by `buildmodel` when `many_files` is set or by `grabdp`. This is a model that reports the frequency of each letter in each state when the training set is evaluated according to the model. See Section 9.3 and Section 10.5.
.fstat
  A scoring file produced by the `fragfinder` program. See Section 10.4.
.hmmer
  An HMMER-format model produced by `sam2hmmer`. See Section 10.10.7.
.kids
  A Kestrel sequence id file. The file is an ordered list of identifiers for sequences in a `.kseq` or `.krseq` file. See Section 10.12.10.
.kseqs
  A Kestrel sequence database, containing an encoding of the sequences optimized for Kestrel `hmmscore`. See Section 10.12.10.
.kseqs
  A Kestrel reverse null model scoring sequence database. This contains each sequence in the original database, plus a reverse of the sequence. See Section 10.12.10.
.match-rdb
  An RDB file created by `grabdp`, listing the posterior match probabilities of each amino acid type at each node, plus the prior probabilities of each amino acid type. Used for diagnostic purposes. See Section 10.5.
.mod
  A model file created by a `buildmodel`, `addfims`, or `modelfromalign`. When `many_files` is not set (the default), `buildmodel` places the run statistics, parameter settings, and the frequency model into this file as well. See Section 9.3.
  .f.mod
    A subfamily model for family number `f'. See Section 9.4.
  .a.mrrr.mod
    If `print_all_models` is set, model number during re-estimate cycle 'rrr' will be placed in the file.
  .s.rrr.mod
    If `print_surg_models` is set, the winning model is printed after each surgery iteration, where `rrr' is the re-estimation index.
.mult
  One of two multiple domain alignment output files created by `hmmscore`. This will contain all alignments to a motif that were found. See Section 10.2.5.
.mlib
  A model library file created by `hmmscore` model calibration. Each entry includes a single- or multi-track model specification and various scoring parameters. See Section 10.2.10.
.mstat
  The other multiple domain output file. This file contains the sequence identifier and scores for the data in the corresponding `.mult` file. See Section 10.2.5.
.pa2m
  A SAM alignment file that alternates sequences and posterior probability annotations in sequence format, as created by `pathprobs`. See Section 10.8.
.pdoc
  Created by `grabdp`, this file contains the posterior decoding of the dynamic programming for match states and transitions into match states. The files tend to be rather large. See Section 10.5.
.plt
  A `gnuplot` command file created by `makehist`. See Section 10.11.
.ptrack
  Created by `predict_track`, this file contains secondary structure (or other second alphabet) predictions for a given sequence based on a primary sequence model, and databases of primary and secondary structure for a group of sequences. See Section 10.9.
.samrc
  A file of default parameters either in a home directory or the current directory. See Section 6.
.sel
  Sequences that passed the selection criteria used in `hmmscore`. See Section 10.2.
.seq
  A file of sequences, as for example created by `sampleseqs`.
.stat
  The statistics of a `buildmodel` run when `many_files` is set, including re-estimation scores and initial parameters. See Section 9.3.
.ta2m
  An alignment trimmed by the `pathprobs` program. See Section 10.8.
.weightoutput
  A list of sequence weights from the internal weighting option of `buildmodel`. Present when `print_all_weights` and internal weighting are both enabled. See Section 9.4.4.

The following file extensions are conventionally used in this manual.

.colors
  A color file for the `makelogo` program, usually located in the same directory as the Dirichlet priors. See Section 10.10.4.
.log
  Standard error output from running `target2k` can be redirected to this file. See Section 4.
.ncomp
  A Dirichlet mixture prior library file, where n is the number of components to the mixture, as in `null.1comp` or `mall-opt.9comp`. Information on specific mixtures can be found at `http://www.cse.ucsc.edu/research/compbio/dirichlets/index.html`. See Section 8.1.
.plib
  A Dirichlet mixture prior library file (old naming convention). The same extension is used both for match state regularizers and HSSP-based transition regularizers. See Section 8.1.
.pretty
  The output (stdout) from `prettyalign`. See Section 10.1.
.regularizer
  A transition regularizer, generally used in conjunction with a Dirichlet mixture regularizer for the match states. See Section 8.1.
.weights
  A file of sequence weights. See Section 9.4.

In most cases, SAM can read compressed (.gz or .Z) files, specified either as their complete name or as their root name without the compression suffix. If the root name is given and both a compressed and an uncompressed file exist, the uncompressed file is read. If both a .gz and a .Z file is present, the .gz file is used. Reading compressed files requires that the GNU decompression program `gunzip` and the Unix decompression program `uncompress` be in the user's path.

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