Se qS el

A Sequence and Structure

Coloring Format

Note: The SCF format (.scf) has been renamed to the SeqSel format (.seqsel) due to preexisting SCF formats that store data from DNA sequencing instruments. The .scf extension is still compatible with jevtrace.

The SeqSel sequence coloring format is designed to encode the coloring of individual sequences, multiple sequence alignments (MSA) and protein structures.

SeqSel is compatible with multiple types of alignments and structures, encoding universal features. The format is text based, human readable, and optimized for storage. Since the coloring data is valid only for a specific sequence or alignment, an optional checksum is added to each selection file to ensure consistency.

SeqSel

x1 x2 y1 y2 r g b

where (x1,y1) and (x2,y2) are alignment coordinates of the residue or alignment block

and

r,g,b are the Red Green and Blue RGB color channels.

SeqSel has been published in Genome Biology in the Jevtrace publication. Jevtrace is a Java implementation of a comparative and structural genomic analysis platform, including variations of the Evolutionary Trace method.

Example coloring implementation screenshot

SeqSelis distributed under a GNU open source license:

download the compressed SCFv2.1 Java source and binary class package

Se qSel was created by

Marcin Joachimiak

©University of California Regents.

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This page last updated 02/24/07.