Sequence Coloring Format SCFv1.0 Specification

SCF was created by Marcin Joachimiak, in the Fred E. Cohen Laboratory, Department of Cellular and Molecular Pharmacology, UCSF, San Franscisco.

 

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This page last updated 6.19.01.

The SCF format consists of six columns which are space or tab delimited and end with a newline or carriage return.

 

X1 <tab> X2 <tab> Y1 <tab> Y2 <tab> R <tab> G < tab> B <tab> (optional) C

X1 & X2 are integers between between 1 and n.

Y1 & Y2 are integers between 0 and the m.

R, G, B are integers between 0 and 255.

 

X1 = integer representing the position in the sequence or multiple sequence alignment

X2 = X2=X1 if selecting one position (Figure 1), otherwise X2 > X1 and defines a rabge of positions (Figure 2)

Y1 = integer representing the sequence or ALL sequences (Y1=0)

Y2 = Y2=Y1=0 if selecting a position in all sequences, Y2=Y1 if selecting a single sequence (Figure 1), otherwise Y2 > Y1 and defines a range of sequences (Figure 2)

R = red value of 24 bit RGB color

G = green value of 24 bit RGB color

B = blue value of 24 bit RGB color

C = optional comment starting with the characters '//', good to limit to < 50 chars

• positions in a sequence are counted from 1 to n, left to right, where n is the length of the sequence (or sequence alignment).
• sequences are counted from 1 to m, top to bottom, where m is the number of sequences.
• the alignment file does not change for a given SCF sequence selection, that is the lengths, orders and gaps remain the same. This is ensured by a checksum variable in the JAVA(tm) implementation of SCF.

Figure 2

Representation of a block selection with SCF.

Figure 1

An individual amino acid in a single sequence selection represented in SCF.

 

download example SCFv1.0 flatfile