Dear all, I am using mercator+mavid ( as discripted in "Aligning Multiple Whole Genomes with Mercator and MAVID" Appendix A) for generating input files for Gbrowse_syn. So once 'mavidAlignDirs' run, How can I extract the whole genome alignment sequences in ClusterW format for Gbrowse_syn? Out of two genome I have, one is in draft version. How can i retrieve the sequence after the comparative scaffolding ? I could see the scaffolding in .agp file, but is there any script for retrieving sequence in assembled ?
I mailed the same to the auther and waiting for his reply. Mean while if any one of you have experienced the same then please guide me.
If you have any other suggestions or comments (eg: pecan), please let me know. I have selected this approach since it has an advantage of comparative scaffolding. But my main objective is to make a synteny gbrowse
Dear all
I am trying to make synteny analysis on e.coli and mycobacteria with its entire strains. I downloaded data from NCBI Ftp site. some organism having multiple genome but in one genome it is having thousands of genes listed separately. As a new student to this field I don't know make MSA with two organisms which having more than one genome and each genome carrying separate genes inside it. Final results should be in .aln format. Please help me a way out
Regards