Pseudogenes are those sequences in the genome that bear similarity to specific protein coding genes, but nevertheless are unable to produce functional proteins due to existence of frameshifts, prema- ture stop codons or other deleterious mutations (Mighell et al., 2000). While I doing some research on protein PLEKHA7, I use the PseudoPipe(an automated pseudogene identification pipeline)(Zhang et al.,2006) to find out the pseudogenes of PLEKHA7. But I am confused that the DNA sequence is 226929bps in length, its pseudogene is only about 100bps long but with a much higher identification like 41.1% and 71%.Result from PseudoPipeResult from PseudoPipe (chr = chromosomes,start = start position,end = end position,query = parent protein,frac = fraction of the parent protein that is overlapping with the pseudogene,ins = number of insertions in the pseudogene sequence,del = number of deletions in the pseudogene sequence,shift = number of frame shifts in the pseudogene sequence compared to parent,stop = number of stop codons in the pseudogene sequence,expect = e-value for the sequence identity between parent and pseudogene,ident = sequence identity between parent and pseudogene,polyA= presence of polyA signal,type = pseudogene biotype : PSSD = processed, DUP = duplicated, FRAG = ambiguous ) So how does these pseudogenes have such high identification to the parent gene as they are only very short sequences?

  • $\begingroup$ It would probably much easier for us if you could paste the relevant lines in plaintext and also add a link to the specifications of the output file. $\endgroup$ – cel Oct 2 '15 at 14:21

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