GeneBander: integrated graphical representation of CG, CpG, Blast, ...
What does this tool do? - Sample output - Gene discovery with GeneBander - Annotation tutorial - Gallery

A free integrated gene discovery tool providing graphical representation of
CG isochores, CpG islands, GenScan, RepeatMasker, Blast, GenBank, ClustalW, SwissProt, genomes, genes,
exons, introns, ESTs, alignments, mutations, synteny, species comparisons, homologies, protein domains
, ...

Upload a file :

Or paste in accession number:

Or paste in nucleotide sequence

Graphical bands wanted:

...CG isochores
...CpG islands
...Other features

Output order for graphical bands (top to bottom):

... CG isochores
... CpG islands
... RepeatMasker (requires table)
... GenScan (requires table)
... Feature tables
...Vertical output
Optionally, paste in feature tables:
... :1 Final scale (bp per pixel)
... Height per band (pixels)
... Band gap (pixels)

Do I have to pay or register? No. GeneBander is an open source web tool freely accessible to everyone. Questions? Click here.

What does this tool do? It replaces designated features in the input sequence by vertical bars one pixel wide and replaces remaining sequence with blanks. Next, the graphic is compressed to the desired scale (eg, 40:1), leading to gray scale (averaged) values for pixels. The final graphic is screen-size,750 pixels wide and total height equal the number of bands x height of band requested.

Gene discovery with GeneBander: The output graphic is designed to help annotate genomic sequences. It arranges many kinds of data derived from the sequence in registered bands. This allows quick visual comparison of whether a GenScan exon prediction lies within a RepeatMasker retrotransposon or has Blast support etc. Users can band many kinds of data in any order. Some people align gene prediction output from many tools (XGrail, Genefinder,... ) To visualize a known gene, simply use annotation data at GenBank.

Sample output: The example shows 12 bands of output from a pseudogene sequence downstream of the prion gene on human chromosome 20. The scale is 40:1 which means 30,000 bp of sequence give a graphic of width 750 pixels. The output could have been made vertical by checking the designated input box.

Gallery: Some examples of GeneBander at work are collected below (see the annotation tutorial for details). GeneBander examples can also be submitted by visitors. Send a web link and brief explanation to your finished graphic and its accompaning annotation. (Do not email graphics themselves, just the link to them.) Links to interesting examples will be posted here.

Prion gene. Point mutations relative to CpG mutational hotspots. Basic
KIAA0128: a new gene on human chromosome 20. Both DNA and protein
Dynein: a pseudogene consisting solely of 3'UTR. Fancy
Examples of feature tables: A feature table is a column of numbers giving feature start and stop positions. These are used to mask your input sequence. GC isochores, CpG islands, and masked RepeatMasker bands are calculated directly from the input sequences and do not need a table. Many tables can be pasted in at one time: order in determines order out in the graphic.

If the text below were pasted in the feature tables box, individual output bands on a gray background would be calculated for RepeatMasker (RM), GenScan(GS), point mutation locations (MU), Blastn matches (BN), and GenBank annotations (GB); the 2-letter code you choose will appear as legend within the graphic. Each table must have a header (>2-letter plus total sequence length) followed by pairs of numbers separated by a blank describing the features. Be sure to follow input format exactly.

>GS 499
27 89
112 345
432 499

>MU 299
123 123
234 234

>BN 345
23 34

>GB 999
345 688
905 944
More advanced feature tables allow banding of strand orientation and coloring of feature subtypes within a band, all in one step. For example, RepeatMasker output provides start, stop, plus or minus strand, and repeat type. GenScan predictions give strand orientation and type (promoter, exon, poly A, etc.]. ClustalW alignments give identity and similarity in amino acid matches and so on. Input for making these more advanced bands consists of start, stop, + or -, and color-wanted data. Eight colors are supported: black, white, red, blue, green, magenta, cyan, yellow.

In the RepeatMasker example below of a 799 bp sequence, SINEs were wanted in red and LINEs in blue. The output will be a single split band with positive strand matches above and negative below. In the ClustalW example, alignment of two proteins of length 457 will be output with identities in green and similarities in yellow. In the GenScan example of 567 bp, plus strand exons will be output in cyan, the promoter in magenta, and the poly A in red.

Fancy input tables are quickly built within a simple spreadsheet using search and replace tools to process output of the original source. Be sure to follow input format exactly.

>RM 799
123 345 + red
456 567 - blue
678 789 - red

>CW 457
123 123 yellow
234 234 yellow
456 456 green

>GS 567
23 59 + magenta
67 89 + cyan
99 101 + cyan
144 167 + red

Ackowledgements: GeneBander was conceived by xyz; its algorithm written and supported by pqr; the web site was designed by mno; questions will be answered (maybe) by efg. GeneBander can run locally on UNIX or LINUX systems. It is free to academic and non-profit institutions (contact hij).