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. BasicExamples 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.
KIAA0128: a new gene on human chromosome 20. Both DNA and protein
Dynein: a pseudogene consisting solely of 3'UTR. Fancy
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 944More 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).