Dear Tlatmil, I have not used this tool before. Mapping tools in general rely on some form of valid alignment threshold and scoring matrices (which may reveal biologically reasonable mapping). If you had not looked into varying the threshold or conditions for permitted alignments, may be you can attempt this and see what you get. If there is already a known region of homology you are aware of, you can track that as a positive control.
Since your are aligning a genomic scaffold to a complete genome, could it be that these regions of interest are missing in your assembly? HTH Mbandi S.k --------------------------------- Universiteit van wes kaapland Suid-Afrika P.S I also followed a presentation in which circos (http://www.circos.ca) was use for visualizing genome alignments. However, do not know if the alignments and genrated in circos. > Hi all, > > Maybe you can help me in this matter : > > I would like to find orthologous regions between genomic scaffolds and > complete genome (e.g., mm9/hg19). I understand this can be done with > blastz or lastz - which is the recommended one and can also do some > chaining. I have up to 30 processors available on Linux, but I'm not > connected to any grid at this point. I played a bit with lastz but I'm not > getting biologically reasonable mapping. Basically, I just need to find > for each scaffold which genomic region is its estimated ortholog, in order > to map genes into the scaffold and test their parallel synteny. > > Is it possible under this conditions to do that ? is there any > instuction/pipeline for that ? > > thanks > Tlatmil > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
