result of cd hit est 2d meaning

Question

[nasromer2191989]

Hi everyone I use the cd hit est 2d to compare two file which is work fine but there minus sight beside of the percentage I couldn't understand. -/95.45% +/95.65%

any one have an idea

Thanks

Answer 1

[ALchEmiXt]

The minus comes before the percentage identity and indicates orientation of the alignment of the subsequence (first two coordinates) to the cluster representative (*) the next two coordinates. See also http://seqanswers.com/forums/showpost.php?p=117497&postcount=2

[nasromer2191989]

Hi ALchEmiXt In my case I want to know what the plus and minus indicate.Why in the first one is minus and in the second one plus.I did not find the explanation for that

22nt, >hsa-miR-122-5p... * 22nt, >hsa-miR-3591-3p... at -/95.45%

0 22nt, >hsa-miR-1-3p... * 1 22nt, >hsa-miR-1-3p... at +/100.00%

Thanks

[ALchEmiXt]

I think it means exact the same. It should be the orientation of the alignment of the sequence in question relative to the sequence marked as the sequence representative. You could easily check this if you replace the cluster representant sequence with its reverse complement sequence. In that case all + should become - and vise versa.... Even though I have to say I only used CD-HIT in other AA modes.... Another option is to post a short example of demo seq and how you run it. We could reproduce and help to understand. The documentation of CD-HIT is not that elaborate....

[nasromer2191989]

Hi ALchEmiXt

Please do you have link of the paper to use as reference of that explanation. I appreciate all your responding.

Thanks again