Output formats¶
Instead of the pretty display output, MView can write several useful multiple alignment formats.
Any row or column filtering options will be respected, so you can also extract subsets of sequences (see Filtering rows), or particular alignment blocks or strand oriented data from blast or similar (see the various sequence database search input formats).
plain¶
A simple multiple sequence alignment format.
MView option: -out plain
This is composed of rows of identifier and sequence in two columns like:
id1 sequence1 id2 sequence2 id3 sequence3
and can contain comment lines starting with #
. Identifiers and sequences
must not contain any whitespace as this is used to separate the columns. The
input sequences need not be aligned vertically, but they must all be the same
length. Use -
and/or .
characters for gaps.
mview¶
An annotated multiple sequence alignment format (the default).
MView option: -out mview
This is composed of rows of row number, identifier, annotations and sequence in multiple columns like:
num1 id1 annotation1a annotation1b ... sequence1 num2 id2 annotation2a annotation2b ... sequence2 num3 id3 annotation3a annotation3b ... sequence3
with the same restraints as plain
format. The annotation columns are
things like percent coverage, percent identity, sequence description,
orientation, etc., and vary with input data source.
FASTA¶
The classic FASTA (or Pearson) sequence file format.
MView option: -out fasta
or -out pearson
.
CLUSTAL/aln¶
The CLUSTAL multiple sequence alignment format (version 2.1, as produced by clustalx-2.1).
MView option: -out clustal
or -out aln
.
Output includes end of row numbers and a Clustal-style *:.
amino acid
conservation line: *
for full column identity, and :
or .
for
strong and weak amino acid grouping, respectively, as defined in CLUSTAL.
For DNA or RNA sequences, if the molecule type was set to nucleic acid with
-moltype na
or dna
or rna
, then the clustal conservation line will
show only the column identities.
PIR¶
The Protein Information Resource sequence file format.
MView option: -out pir
This format includes a molecule type annotation. If the -moltype
option is
set (one of aa
, dna
, rna
, na
), MView will try to output a
reasonable value (P1, DL, RL, XX; for protein, linear DNA, linear RNA, or
unknown, respectively). The default is protein.
MSF¶
The Wisconsin Package GCG Multiple Sequence File format.
MView option: -out msf
This format includes a molecule type annotation. If the -moltype
option is
set (one of aa
, dna
, rna
, na
), MView will output the right
value (P or N; for protein or nucleic acid). The default is protein.
RDB¶
MView option -out rdb
A tab-separated format including scoring information. RDB is a CSV-style format with header lines giving column name and type information (see rdb).