Chromosome Translocations Simulation

Question

[Ma]

Hi: I want to simulate chromosome translocations by using the FASTA files available in NCBI. For example for the Philadelphia chromosome I know that is the union of BCR (chromosome 22) and ABL (chromosome 9) that their fusion form the ph chromosome. In that case the simulation that I did was to download the fasta sequences of chromosome 22, gene BCR, gene ABL; and then join BCR+ABL to the chromosome 22 in their last segment (the part corresponding to the BCR point). The problem that I got is when I want to simulate for example the Ewing´s sarcoma, that is the product of the following translocation t(21;22)(q22;q12) I have read that the Ewing´s sarcoma there is the fusion of the genes EWS (chromosome 22) and ERG (chromosome 21) so I got the fasta file of both genes. The question is if I also the fasta files of chromosome 21 and 22, how I can generate a fasta file that resembles this translocation? I just need the description of the procedure and no programming code at all. Also is there any database where one can download this chimeric chromosomes in fasta format? Thanks

[Larry_Parnell]

There have been a few such quesitons on this forum in the last month or so on BCR-ABL sequences. Please use the search function to find those questions, whose responses should be able to guide you.

Answer 1

[Sean Davis]

Have a look at Chimerdb, perhaps.

[Ma]

I have looked at Chimerdb, but the information is a little bit scarced, only links to another papers that I could found in NCBI for example

Answer 2

[Benm]

Maybe this script of mine - simulateSeq.pl would help you.

[Ma]

thanks, can you explain me a little bit what does your script do and how to use it?

[Benm]

you can look for the details from the README: http://sourceforge.net/projects/simulateseq/files/0.2.2/

or just run the command:

perl simulateSeq.pl --Example that would give you some example in order to understand it well.

And your requirements can be set by " Mutation parameters ", such as "--Tran <int[-start:int-end:int-size:int]&gt; set="" Translocation="" variation="" number"<="" p="">