Alignment manipulation programs

BMERC : needle tools : Programs : Alignment programs

See the Threading alignment experiments page for more information on how needle uses alignments.

Table of contents

1. Alignment manipulation programs
   1. Table of contents
   2. fssp-core-corr.pl
   3. correct-alignment.pl
   4. align.pl
   5. pima-multi-align.pl
   6. pima2fssp.pl
   7. make-align-depends.pl

Usage:

    fssp-core-corr.pl [-verbose] [-print-align]
                [-use-fssp-structural-equivalence] [-fssp fssp-file-name]
                -core1 core-file-name-1 -core2 core-file-name-2
                [-locus1 locus-name-1] [-locus2 locus-name-2]

Arguments:

-use-fssp-structural-equivalence

if specified, uses FSSP definitions of structural equivalence, indicated by case in the alignment. If this option is given, only columns in the alignment where both residues are in uppercase are considered; otherwise, case is ignored. The default is not to require structural equivalence (which is probably a mistake).

-core1 core-file-name-1

name of the first "core" format file, e.g. "2mhr.core", required for input.

-locus1 locus-name-1

specifies a locus name for the first core. If omitted, the file name minus the extension and directory (e.g. "2mhr" for "../2mhr.core") is used (but the name must contain at least one dot).

-core2 core-file-name-2

name of the second "core" format file, e.g. "2mhr.core", required for input.

-locus2 locus-name-2

specifies a locus name for the second core. If omitted, the file name minus the extension and directory (e.g. "2mhr" for "../2mhr.core") is used (but the name must contain at least one dot).

-fssp fssp-file-name

specifies the FSSP-format alignment file to use; if not specified, this is read from the standard input.

-print-align

if specified, this boolean option causes the original FSSP alignment to be printed in multiple alignment format, along with the secondary structures as defined by the core files. After this alignment is printed, fssp-core-corr.pl exits immediately, and does not produce ctimap output.

-verbose

if specified, causes the -print-align alignment to be printed, and uses a three-column output format which includes mappings where a given aligned position belongs to either core, instead of requiring both. This is useful only for debugging.

    insert1----------
    -------insertion2

Usage:

    correct-alignment.pl [-verbose] [-preserve-case] [-fssp fssp-file-name]
                [-seq1 seq-file-name-1] [-seq2 seq-file-name-2]

Arguments:

-fssp fssp-file-name

specifies the FSSP-format alignment file to read; if not specified, this is read from the standard input.

-seq1 seq-file-name-1

-seq2 seq-file-name-2

specifies the name of a sequence file to use to correct one of the sequences in the alignment; either or both may be specified. In fact, the sequence name stored in the file is what is used to decide which aligned sequence to correct, so it doesn't matter which is sequence 1 and which is sequence 2. (If neither sequence file is specified, the original alignment is regurgitated.)

-preserve-case

if specified, case is preserved for residues inserted from the additional sequence(s). Otherwise, the default is to apply the FSSP convention of lowercase to indicate "structurally nonequivalent" residues.

-verbose

if specified, causes extra debugging information to be printed.

Known bugs:

1. *** Sequence names (labels) in sequence files must match the sequence names in the FSSP file, the way the thing is currently written. In a sense, this is a feature, because you don't have to know in what order the sequences appear in the alignment. But it's a bug if you do know and need to use that to override mismatched sequence names.

Usage:

	align.pl seq1 [ seq2 ]

Arguments:

seq1

name of the first IG format file, e.g. "2mhr.seq", required for input.

seq2

name of the second IG format file; this comes from the standard input if omitted.

Known problems:

1. At present, align.pl converts the sequence to uppercase, which makes it unsuitable for patterns. -- rgr, 15-Sep-99. [I think this only applies if you use the unpatched version of the globalS program. -- rgr, 29-Oct-99.]

-verbose

If specified, produces debugging output. May be specified multiple times to increase the amount of output.

-help

Prints a brief help message, and exits.

-html-help

Prints a brief help message in HTML, and exits.

-tbl sequence-file

Name of a .tbl format file of sequences. Required, and cannot be '-', since pima-multi-align.pl must both read the file and pass it to pima_align as well.

-pima pima-alignment-file

Name of a PIMA .align file, in lieu of running pima_profile on sequence-file. If pima-alignment-file is specified, -pscore is not needed.

-pscore pima-pscore-file

.pScore file name to pass to pima_profile. Cannot be '-' (standard input) due to pima_profile limitations.

-markup markup-file-name

Reads HTML markup replacement instructions from the named file. This file should contain the initial text and the replacement, separated by tabs, one pair per line.

Usage:

	pima2fssp.pl [-locus1 new-locus1] [-locus2 new-locus2]
                [ pima-alignment-file ]

Arguments:

-locus1 new-locus1

optionally specifies a new locus name to override whatever pima2fssp.pl found in the first sequence file.

-locus2 new-locus2

optionally specifies a new locus name to override whatever pima2fssp.pl found in the second sequence file.

pima-alignment-file

name of an input PIMA alignment file; if not specified, standard input is read.