Create fusion transcripts with breakpoint coordinates from two genes.

Question

[simplitia]

Hi given a gene fusion coordinate as such

chr11:HSPA8:122929766:-| chr12:UBC:125398320:-|fusion

is there a tool that can create a fusion mRNA from the above coordinate? Even better if i can detect if its in-frame. so ideally it would give me the sequence starting with ATG start site of HSPA8, end at the predicted junction coordinate and fuse this with sequence UBC and ending with UBC stop codon.

For exampe, currently I do it manually. Which is the find the sequence for both HSPA8 and UBC, go to ucsc and extract the junction sequences, see where it is at relative the the gene seqeunce, extact the appropriate sequences and combined them. all.manually. Is there a script for this? Thanks.

Alex