Re: [Artemis-users] ACT comparisons
Hi Magdalen Sorry to hear you are having trouble with WebACT. I have tried it a couple of times and it is working for me. It may be a temporary glitch or possibly an issue with the size of the sequence. It may be worth trying again? Regards Tim On 2/16/11 3:34 PM, "Bossers, Alex" wrote: > Magdalen, > not sure if its supported but we successfully use MUMmer locally (or blast+) > to generate the required comparison files. > Best wishes, > Alex > > > Van: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk] > namens Magdalen Lindeberg [m...@cornell.edu] > Verzonden: woensdag 16 februari 2011 15:32 > Aan: artemis-users@sanger.ac.uk > Onderwerp: [Artemis-users] ACT comparisons > > After years of using the ³Generate² feature at WebACT > http://www.webact.org/WebACT/generate for generating ACT readable comparison > files, my recent attempts to generate comparisons with this feature have not > been successful (basically, the comparison generator never concludes the job). > Fortunately, I can get results with DoubleACT, but the output is not as > convenient. > > Does anyone know if WebACT is still being supported? No one is responding to > the ³contact us² link. > > thanks, > Magdalen > > Magdalen Lindeberg PhD > Department of Plant Pathology and Plant-Microbe Interactions > 302A Plant Science Building > Cornell University > Ithaca NY 14853 > > http://pseudomonas-syringae.org > http://www.citrusgreening.org > > > > ___ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] ACT comparisons
Magdalen, not sure if its supported but we successfully use MUMmer locally (or blast+) to generate the required comparison files. Best wishes, Alex Van: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk] namens Magdalen Lindeberg [m...@cornell.edu] Verzonden: woensdag 16 februari 2011 15:32 Aan: artemis-users@sanger.ac.uk Onderwerp: [Artemis-users] ACT comparisons After years of using the “Generate” feature at WebACT http://www.webact.org/WebACT/generate for generating ACT readable comparison files, my recent attempts to generate comparisons with this feature have not been successful (basically, the comparison generator never concludes the job). Fortunately, I can get results with DoubleACT, but the output is not as convenient. Does anyone know if WebACT is still being supported? No one is responding to the “contact us” link. thanks, Magdalen Magdalen Lindeberg PhD Department of Plant Pathology and Plant-Microbe Interactions 302A Plant Science Building Cornell University Ithaca NY 14853 http://pseudomonas-syringae.org http://www.citrusgreening.org ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] ACT comparisons
After years of using the "Generate" feature at WebACT http://www.webact.org/WebACT/generate for generating ACT readable comparison files, my recent attempts to generate comparisons with this feature have not been successful (basically, the comparison generator never concludes the job). Fortunately, I can get results with DoubleACT, but the output is not as convenient. Does anyone know if WebACT is still being supported? No one is responding to the "contact us" link. thanks, Magdalen Magdalen Lindeberg PhD Department of Plant Pathology and Plant-Microbe Interactions 302A Plant Science Building Cornell University Ithaca NY 14853 http://pseudomonas-syringae.org http://www.citrusgreening.org ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[artemis-users] ACT comparisons -
Hello, I am trying to do an ACT comparison using big_blast on two constructions of the same partial genome (one with 4 contigs and one with 3 to see where the various pieces have been joined together). I was therefore expecting large blocks of identical sequence showing rearrangement etc. However, I seem to be getting loads of small blocks. I think that of this is due to multiple repeat elements but I was wondering if it was something to do with the window size used by blastn or the block size by big_blast. Does anyone have any suggestions on how to improve the layout? Thanks in advance Melanie Duffield Bioinformatics Biomedical Sciences Porton Down Wilts SP4 0JQ Tel (1)980 614364 Fax (1)980 614307 "This e-mail is intended for the recipient only. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely upon this e-mail. If an addressing or transmission error has misdirected this e-mail, please notify the author by replying to this e-mail." "Recipients should note that all e-mail traffic on MOD systems is subject to monitoring and auditing."
