Consult about multiple alignments
zhang...@ioz.ac.cn
Dear professor:
I have encountered some problems and confusions about multiple alignments and I want to ask you for advice. Recently I want to align the genome sequences of multiple species in Tephritidae,so I find “https://github.com/ucscGenomeBrowser/kent.git” and run the doBlastzChainNet.pl. However,the program have not run successfully on my server. Then I have used Lastz and got the alignment file (figure 1). When I compare it with the “maf” file download from “Multiple alignments of 124 insects with D. melanogaster”（figure 2）,I find that my file lack lines begin with “i”. What should I do to generate this information? Is there some programs that can generate this information in “kent.git”? Looking forward to your reply,thank you!
Sincerely,
Dr. Zhang
figure 1
figure 2
Gerardo Perez
Hello, Dr. Zhang.
Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.
We can direct you to our makedoc, which details all the operations and programs used to create the dm6 multiz 124-way alignment. Please note that this document is primarily intended for internal replication. You can access the makedoc on GitHub here: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/dm6/multiz124way.txt
For lines beginning with "i", refer to the GAP ANNOTATE MULTIZ124WAY MAF AND LOAD TABLES (DONE - 2017-11-23 - Hiram) section of the makedoc, which you can find here: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/dm6/multiz124way.txt#L1778
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/4f441b13.ccdc.193b9e7c0c1.Coremail.zhangjingyi%40ioz.ac.cn.