12.3 Details of EMBOSS Programs

12.3 Details of EMBOSS Programs

The programs are listed alphabetically. A description, example, and summary of the command-line arguments are given. Optional and advanced qualifiers are listed if applicable.

General qualifiers: (used by all programs)

-help (boolean)

Report command line options. More information on associated and general qualifiers can be found with -help -verbose.


aaextractindex extracts information from the AAINDEX database for use by pepwindow and pepwindowall. AAINDEX is a database containing properties of amino acids. The AAINDEX database file aaindex1 can be downloaded from ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1.

Here is a sample session with aaindexextract:

% aaindexextract
Extract data from AAINDEX
Full pathname of file aaindex1: ~/aaindex1

Mandatory qualifiers:

[-inf] (infile)

Full pathname of file aaindex1.


abiview reads an ABI sequence trace file and displays the results as a graphic.

Here is a sample session with abiview:

% abiview
Name of the ABI trace file: ba16d2.s1
Output sequence [outfile.fasta]:
Graph type [x11]:

Mandatory qualifiers:

[-fname] (infile)

Name of the ABI trace file.

[-outseq] (seqout)

Sequence file.

-graph (xygraph)

Graph type.

Optional qualifiers:

-startbase (integer)

First base to report or display.

-endbase (integer)

Last sequence base to report or display. If the default is set to zero, the value of this qualifier is taken as the maximum number of bases.

-yticks (boolean)

Display y-axis ticks.

-[no]sequence (boolean)

Display the sequence on the graph.

-window (integer)

Sequence display window size.

-bases (string)

Base graphs to be displayed.

Advanced qualifiers:

-separate (boolean)

Separate the trace graphs for the 4 bases.


alignwrap aligns a set of sequences to a seed alignment. This package is still being developed.

Here is a sample session with alignwrap:

% alignwrap

Mandatory qualifiers:

-inpath (string)

Directory containing the seed alignments (input).

-extn (string)

File extension of seed alignment files (input).

-scopfamilies (string)

scop families file containing the set of sequences in EMBL-like format.

-outpath (string)

Directory for extended alignments (output).

-outextn (string)

File extension of extended alignment files (output).


antigenic predicts potentially antigenic regions of a protein sequence.

Here is a sample session with antigenic:

% antigenic
Finds antigenic sites in proteins
Input sequence: sw:act1_fugru
Minimum length [6]:
Output file [act1_fugru.antigenic]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-minlen (integer)

Minimum length.

[-outfile] (report)

Output report filename.


backtranseq takes a protein sequence and makes a best estimate of the likely nucleic acid sequence it may have come from.

Here is a sample session with backtranseq. Note that this is a human protein, so the default (human) codon frequency file is used:

% backtranseq
Back translate a protein sequence
Input sequence: sw:opsd_human
Output sequence [opsd_human.fasta]:

Here is a session using a drosophila sequence and codon table:

% backtranseq -cfile Edrosophila.cut
Back translate a protein sequence
Input sequence: sw:ach2_drome
Output sequence [ach2_drome.fasta]:

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

[-outfile] (seqout)

Output sequence USA.

Optional qualifiers:

-cfile (codon)

Codon usage table name.