Name

feature-map

1997-98 by

Description and concept definitions

Feature map draws a graphical map of a series of features. Given the diversity of feature types, we will illustrate this with a few examples:

• Regulatory sites: each map represents a DNA sequence located upstream a given ORF. Each regulatory site constitutes a feature.
• Swissprot records each map represents a proteic sequence. Each swissprot feature (dna-binding domain, mutagen, ...) constitutes a feature.
• Multiple alignment each map is a sequence (several maps are drawn in parallel), and each aminoacid is a feature.
Several maps can be drawn in parallel, allowing to detect conserved positions across them.

Options

Feature map format
In the standard input format, each feature is represented by a single line, which must contain the following information:
1. - map name (eg: gene name),
2. - feature type (site, ORF),
3. - identifier(ex: GATA_box, Abf1_site)
4. - strand (D for Direct, R for Reverse),
5. - start position (may be negative)
6. - end position (may be negative)
7. - (optional) sequence (ex: AAGATAAGCG)
8. - (optional) score (a real value)
Fields must be provided in this order, separated by tabs.

Feature map also imports result files from some other programs or databases:

• dna-pattern a program which localizes the occurrences of your query patterns within your sequences.
• Matinspector, a program that scans a sequence with a library of matrices for regulatory sites.
• SignalScan, a program which scans your sequences with a librairy of consensus for regulatory sites.
These files are converted into the custom feature-map format before the map is drawn.
Title
The title appears in large fonts at the top of the image. A single line of title is allowed. Its maximal length depends on the image width.

Legend
The legend is drawn at the left top of the image. It indicates the color (and optionally symbol) associated to each feature identifier.

Scale bar
The scale bar appears either under the title (horizontal map) or at the left side of the image (vertical map). It indicates the coordinates. The step is calculated automatically but can also be specified manually.

Sequence names
Write the name besides each sequence.

Orientation
The maps can either be drawn horizontally or vertically.

Display limits
The options from and to define the maximum and minimum coordinated displayed in the map. This allows to zoom on a given part of the graph. If no value are entered, the min and max feature positions are used as limits.

Origin
All coordinates are recalculated relative to this value).

Map dimensions
All dimensions are in pixels.


• Map length refers to either width (horizontal map) or height (vertical map). It is the dimension of the map axis (the sequence backbone).
• Map thickrefers to either height (horizontal map) or with (vertical map). It is calculated automatically according to the content of the map (handles, labels). It can also be adjusted manually.
• Map spacing refers to a margin between maps, which is displayed in the same color as the background.
Warning ! the bigger the surface of the map, the more time is required for its transfer to your client browser.

Feature handle
A color dot or a symbol can be associated to each feature. This is particularly convenient to discernate overlapping features, because the handle are shifted in order to avoid overlap. Black symbols are conveninent to distinguish features on a black and white printing.

Color palette
The default palette assigns one color to each feature identifier (e.g. each pattern). The monochrome palette is convenient for printing feature maps on a balck and white printer, and to avoid publication costs for color pictures.

Color file
Provide a file containing feature-specific colors.
The file contains 2 columns:
1) Feature identifier
2) Red,Green,Blue intensity in a scale from 0 to 255.
This example will assign the red color to all features identified as "Met4p", dark green to features "Pho4p", and very dark blue to features identified as "Met31p".

Met4p	255,0,0
Pho4p	0,128,0
Met31p	0,0,64

Background color (R,G,B)
Specify the color of the background color. Colors are specified with three numbers from 0 to 255, separated by commas, representing the color intensity of the red (R), green (G) and blue (B) channels, respectively. The value 0 means null intensity, and 255 maximal intensity. Some examples:

0,0,0	black
255,255,255	white
255,0,0	red
0,255,0	green
0,0,255	blue
0,0,128	dark blue
128,128,128	grey

Dynamic map
This option requires a recent browser (Netscape 3 or later). When the mous is placed for a second on a given feature, a specific message appears at the bottom of the window, providing all characteristics of this feature (type, position, identifier, description).

Label keys
A label can be written nearby each feature, providing one or several of the following data:

• strand
• position (start and end coordinates),
• identifier
• description
Note that this option gives a better effect with vertical maps, where the labels have less tendency to overlap with each other.

Proportional to score
Feature box thickness reflects the score given in the eight column of the input.

Image format
output format for the image. Supported : png, jpg, ps. The formats jpg and png are bitmap formats, i.e. they are convenient for displaying on a computer screen, but their resolution is restricted to that of a monitor (72 dots per inch). The postscript (ps) format can adapt to the resolutio of any printer.

Credits

feature-map has been written by . This program can be used freely by academic users via its web interface. For commercial users, please read or disclaimer.

feature-map uses the graphical library GD, developed by Thomas Boutell ((boutell@boutell.com).

Copyright statement for the graphical library GD:

	Portions copyright 1994, 1995, 1996, 1997, 1998, by 
	Cold Spring Harbor Laboratory. Funded under Grant P41-RR02188 by the
	National Institutes of Health. 

	Portions copyright 1996, 1997, 1998, by Boutell.Com, Inc. 

	GIF decompression code copyright 1990, 1991, 1993, by David Koblas 
	(koblas@netcom.com). 

	Non-LZW-based GIF compression code copyright 1998, by Hutchison Avenue
	Software Corporation (http://www.hasc.com/, info@hasc.com). 

	Permission has been granted to copy and distribute gd in any context, 
	including a commercial application, provided that this notice is 
	present in user-accessible supporting documentation. 

	This does not affect your ownership of the derived work itself, and 
	the intent is to assure proper credit for the authors of gd, not to 
	interfere with your productive use of gd. If you have questions, ask. 
	"Derived works" includes all programs that utilize the library. 
	Credit must be given in user-accessible documentation. 

	Permission to use, copy, modify, and distribute this software and its 
	documentation for any purpose and without fee is hereby granted, 
	provided that the above copyright notice appear in all copies and 
	that both that copyright notice and this permission notice appear in 
	supporting documentation. This software is provided "as is" without 
	express or implied warranty. 
	

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