How can I load Seqs who do not begin from first base?

[wangshun1121]

For example, I want to compare regions from human, mouse and rat, and the length of the regions I am interested in is only about 500kb or so, but none of these region are at the beginning of Chrs. Then how can I make json from such sequences?

[greatfireball]

Hey @wangshun1121,

Thanks for the question... For a detailed answer, I need to know how do you generate your alignments? Using the default lastz program or do you precalculate the alignments?

Best,
Frank

[wangshun1121]

Well, I can use lastz, but I don't want to align whole chromosome Sequences, I only want to study the short region I am interested in.
For example, I can get the seq of human's Chr01, from 80000000bp to 80500000bp, and align it to rat's Chr02 seq 55000000 to 55500000. Then I want to display the alignments within the short region of 500kb.

[greatfireball]

Thanks for your answer @wangshun1121
I already got the point, that you do not want to align the whole chromosomes against each other. If you are using lastz it seems to be an easy task to implement such a feature. I am testing a little bit and implementing that feature until next week. Hope, that is still okay for you. Nevertheless, offset based alignments are currently not supported by AliTV, therefore I created an issue there: AliTVTeam/AliTV#134. We need to figure out, how to display those alignment offsets. For the moment I will generate a JSON file which can be viewed in AliTV with the drawback, that the positions are translated from their original position (e.g. alignment region are base 100k to150k) into 1-based positions (e.g. bases are shown as 1 to 50k+1).

[wangshun1121]

It's very nice of you @greatfireball ! Look forward to the upgrade of AliTV!