tblastn search parameters

Question

[chevivien]

Hallo guys,

Can someone please suggest to me how I can use the following input search parameters for my tblastn search(using standalone BLAST):

Searching parameters : maximum identity > 95%, length > 200 bp and Evalue < 10e-10 (borrowed idea from http://www.biomedcentral.com/1471-2164/12/76); topic;digital expression analysis.

I am well conversant with the normal input parameters such as

tblastn -db blastdb/nippest -query mydata.fasta -evalue 10e-10 > out.nipest -outfmt 7.

Following the attached paper I wish to add maximum identity>95% and length >200 but I can't figure out...

Thanks.

[Pierre Lindenbaum]

Its a bit complex to understand their usage

then tell us what's your input and what you want to achieve.

P.

[Devon Ryan]

Figure 2b looks like a job for Circos, and figure 1 from the other paper could just be done with Adobe Illustrator (or equivalent).

[chevivien]

Yes figure 2 is circos work, that's what I have been trying to use but got above error messages.. I have posted my question to circos group but I haven't found a solution. But how do you use adobe illustrator to display various gene position in a chromosome?

[Devon Ryan]

The position information in graphics like this doesn't need to be exact (you're not measuring pixels here), so you can just put something together by hand. If you have a lot of positions to plot then this is a no-go, but with just a handful it's likely to be faster than learning a bunch of new packages.

[chevivien]

i got alot of positions to plot...roughly 500 gene duplication positions though some genes duplicated to many genes hence they will share postions.as in gene A gave rise to geneB,geneC and geneD.

[Devon Ryan]

Then you'll need to find or code a solution. For that many positions you'll hopefully be able to get circos to work, since otherwise the image would be too busy to be meaningful.

Answer 1

[Pierre Lindenbaum]

For the question "But how do you use adobe illustrator to display various gene position in a chromosome?" see: Drawing Chromosome Ideograms With Data

inkscape.org is a good alternative to illustrator.

[chevivien]

I want something which can display relationship of varius genes. For example a line connecting duplicated genes (duplicate1 to duplicate 2) as outlined in this papers;

• http://www.ncbi.nlm.nih.gov/pubmed/24609322 Fig 2; or
• http://www.biomedcentral.com/1471-2164/12/76/figure/F1

This post won't give me what I want. I have not used inkscape before let me have a look at it

Thanks Pierre and Devon