Function

Description

prettyseq reads a nucleotide sequence and writes an output file containing in a clean format the sequence with the translation (within specified ranges) displayed beneath it. The translated nucleic acid region is given lower-case letters with the rest of the input sequence left in the input case. A specified codon usage table is used to translate the codons.

Usage

Command line arguments

Input file format

You can specifiy a file of ranges to extract by giving the '-range' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-range @myfile').

The format of the range file is:

• Comment lines start with '#' in the first column.
• Comment lines and blank lines are ignored.
• The line may start with white-space.
• There are two positive (integer) numbers per line separated by one or more space or TAB characters.
• The second number must be greater or equal to the first number.
• There can be optional text after the two numbers to annotate the line.
• White-space before or after the text is removed.

An example range file is:

# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

Output file format

Data files

Notes

By default, the base and residue numbers of the sequence and its translation are shown beside the sequences in the output. There are options to change this behaviour.

The translation will be shown in a number of sequence regions only. The ranges are specified with the -range qualifier. As an alternative to specifying a set of ranges at the command-line, a range file containing such range data may be specified (see "Input File Format").

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

showseq has more options for specifying various ways of displaying a sequence, with or without various ways of translating it.

Author(s)

History

Target users

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