Welcome to twig

This is the first release of twig, Ted's web interface for genomics. It is definitely of alpha quality - it is not particularly user friendly and it needs some more idiot-proofing. Having said that, I use it myself and it is quite functional. Right now, twig is only a tool for aligning cDNA sequence to genomic and annotating the gene. In the future, I plan to add a lot more general functionality to it. If you are interested in the source code, or if you have any problems in general, feel free to mail me

If you are familiar with it, click here for the first page. Otherwise, take the time to read the brief description below.

Following is an outline of the steps involved.

• The first page has a text box into which you can paste your sequence. The sequence should be in fasta format (with or without the header) and should be in all caps, with no weird non-ascii characters.
• After clicking the submit button, you will be taken to the alignment editor. This step takes quite a while! (5-10 min.) Don't despair, just go grab a cup of coffee, and it should be loaded by the time you get back. I will be optimizing this step in the future. The alignment editor presents the alignment of cdna to genomic, with the 5 and 3 prime ends highlighted in yellow, exons in cyan, and introns in magenta. At the top of the page, you will see boxes containing the positions of the start and stop of each exon, which you can change and then update. The page will reload (quickly this time) and you can see the results of the changes you have made. When you are happy with the splice sites as shown, there is a link on this page that will take you to the next step. Be careful - if you have changed any of the numbers in the boxes, make sure to click on the update button before clicking to continue.
• The codon preference calculator takes the exons as set in the previous step, splices them together and computes the codon usage of the gene according to preferences for codon usage in the drosophila genome. This preferences are calculated for each frame, and plotted along with start codons (arrows) and stop codons (circles). Choose the frame with that has consistently high preference, and that has a reasonable arrangement of start and stop codons. At the top of the screen, you will see three boxes (color coded for each frame). Choose the start and stop codon you want from the pull-down menus, and click the corresponding submit button.
• Congratulations! You're done. The final page presents you with several files to download - a fasta format file with cdna and genomic sequence, the alignment produced by clustalw, and a tab delimited table with position of exons, introns, start and stop codons. I should be adding an option to download a full genbank format file soon.