Dear Fred; Thanks for the reply!!!!! extending at the c-terminus means that this protein only N-terminus structure has been solved and I want to include the residues as well in the sequence alignment which are not in the structure.
Regards; Bashir On Fri, November 26, 2010 13:38, Vellieux Frederic wrote: > Muhammed bashir Khan wrote: >> Dear All; >> >> I have structures of two protein one full-length while the other >> truncated >> at the c-terminus(one from prokaryote while the other from eukaryotes). >> Now I want to do the sequence alignment of these two proteins from all >> species in such a way that the structure based sequence remain constant >> while extending the sequence only at the c-terminus. Remember the >> structure are known only for the two proteins. >> >> Any suggestion will be highly appreciated!!!!! >> >> Regards and have a nice weekend. >> >> Bashir >> > Hi there, > > Ages ago, for this type of work (fine-tuning sequence alignments), I was > loading pre-aligned (or not pre-aligned) sequences and was editing the > alignment "by hand" using a sequence alignment editor. This editor was > working on VAX/VMS systems, which no-one uses anymore (I haven't touched > VMS in many many years). > > So I had a look at what sequence alignment editors are available today > using google, and I came across this: Jalview (http://www.jalview.org ). > Unfortunately, it seems it does not wish to install on my Linux box so I > don't know if the software does what you want it to do. And it is not > clear to me exactly what you mean by "extending the sequence only at the > c-terminus". > > Fred. > > -- Muhammad Bashir Khan ************************************************** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522
