about the use of PseudogenePipeline

[wangzhongkai1]

Dear Adam Nunn,
thanks for your contribution on Pseudogene identification, and I'm willing to use it on my own work.
Although I have successfully manage it on my machine, I have two important questions below to solve:

1. Is there any necessity to filter the longest transcript of the coding sequence? what is the influence of this step?
2. In the example configure file you attached, the command line of blast is "tblastn -query test_prot25.fa -db test_genome -out test_prot25_tblastn6 -seg no -outfmt 6", I was wondering if the parameter of "-seg no" would do any good to the results. AND shamefully, I didn't find the deep explanation of this parameter. So could you please help solving my confusion mentioned above?

Thank you a lot, and looking forward to your reply as soon as possible!

[shinhanshiu]

-seg no turned off the low complexity filter. This is crucial because with seg on, some regions will not be aligned and stop/frameshift can be present in those regions.

[wangzhongkai1]

Dear Professor,
thank you for your kindly reply,
I'm now aware of the importance of the -seg parameter, and what about the first question of the longest transcript filtering? Is there any necessity to do this?