Finding pseudogenes in a genomic sequence.
Searching for pseudogenes is performed by aligning set of proteins with the genomic sequence. Protein FASTA-file could contain sequences with unformatted names or (preferably) with specially formatted ones. Proteins with formatted names are produced with a PSF_Pre program (not installed in the current version). This special prot. name format describes nucleotide sequence which translation gives appropriate protein, and number of its exons.
All the alignments containing one of the following are considered pseudogene candidates:
(1) stop-codons/frameshifts in nuc. sequence [for alignment with ANY protein]
(2) PolyA site and/or PolyA signal, if exon is single [for alignment with ANY protein]
(3) Number of exons is much lower than in ancestor gene [for alignment with protein SPECIALLY FORMATTED]
(4) Ka/Ks ratio exceeds 0.5 [for alignment with protein SPECIALLY FORMATTED]
It is recommended to input NR or IPI base as a protein base (better unredundant). In this case only p.(1) and p.(2) will work, but resulting candidates will be more reliable. Note that incorrectly predicted proteins might give a number of false pseudogenes.
chr @@ chain @@ pos(dir.ch.) @@ len(nt.) @@ identity,@@ coverage,@@ Ka/Ks @@ uali.head @@ uali.tail @@ exons#,lower @@ exons#,upper @@ polyA @@ polyA_signal @@ corr.stops# @@ uncorr.stops# @@ corr.frameshifts# @@ uncorr.frameshifts# @@ prototype_chr @@ prototype_prot_name @@ prototype_exon#,lower @@ prototype_exon#,upper @@ DNA_identity @@ CDS length ENm009 @@ - @@ 322971 @@ 859 @@ 57.79 @@ 81.61 @@ 0.283 @@ 0 @@ 13 @@ 1 @@ 1 @@ 0 @@ 0 @@ 0 @@ 0 @@ 0 @@ 1 @@ chr11 @@ C11000184 chr11 1 exon (s) 424011 - 423106 ORF: 1 - 900 299 aa, chain - ## BY PROTMAP: gi|21928977|dbj|BAC06074.1| seven transmembrane helix receptor [Homo ## 29 @@ 1 @@ 1 @@ 60.656 @@ 732 @@ ENm009 @@ + @@ 966139 @@ 872 @@ 49.59 @@ 75.63 @@ 0.487 @@ 10 @@ 19 @@ 1 @@ 2 @@ 0 @@ 0 @@ 0 @@ 0 @@ 0 @@ 1 @@ chr11 @@ C11000197 chr11 1 exon (s) 433690 - 432722 ORF: 242 - 1204 orf 4667288 4668250 320 aa, chain - ## gi|13540539|ref|NP_110401.1| (NM_030774) olfactory receptor, family 51, subfamily E, member 2; prostate specific G-protein coupled receptor [Homo sapiens] ## 320 ## orf_perfect ## NM_030774_#_242_#_1204 @@ 1 @@ 1 @@ 60.882 @@ 726 @@ ENm009 @@ + @@ 33573 @@ 928 @@ 62.29 @@ 95.19 @@ 0.284 @@ 3 @@ 1 @@ 1 @@ 1 @@ 0 @@ 0 @@ 0 @@ 0 @@ 0 @@ 1 @@ chr11 @@ C11000202 chr11 1 exon (s) 437411 - 436467 ORF: 1 - 939 312 aa, chain - ## BY PROTMAP: gi|22061831|ref|XP_171424.1| similar to olfactory receptor [Pan trog ## 31 @@ 1 @@ 1 @@ 66.105 @@ 891 @@ ....
| chr | chromosome (or another sequence) name is which search has been carried out |
| chain | chain |
| pos(dir.ch.) | (nt.) pseudogene start position (in direct chain) |
| len(nt.) |
(nt.) pseudogene length. Note thate pseudogene lies from the right of 'pos(dir.ch)' |
| identity | (%) Identity with a protein (0...100%). |
| coverage | (%) Coverage of a protein with alignment |
| Ka/Ks | ratio calulated by Nei-Gojobori method |
| uali.head | (yes/no) first codon of alignment is ATG |
| uali.tail | (yes/no) last codon of alignment is stop-codon |
| exons#,lower | number of exons, lower estimation |
| exons#,upper | number of exons, upper estimation |
| polyA |
(yes/no) there is a polyA tail at the 3' terminus of alignment |
| polyA_signal |
(yes/no) there is a polyA signal at the 3' terminus of alignment |
| corr.stops# | number of correctable (by one mismatch) in-frame stop codons |
| uncorr.stops# | number of uncorrectable (by one mismatch) in-frame stop codons |
| corr.frameshifts# | number of correctable (by one-nucleotide instertion/deletion) frameshifts |
| uncorr.frameshifts# | number of incorrectable (by one-nucleotide instertion/deletion) frameshifts |
| prototype_chr | chromosome of prototype protein gene |
| prototype_prot_name | prototype protein gene name |
| prototype_exon#,lower | number of exons of prototype prot. gene, lower estimation |
| prototype_exon#,upper | number of exons of prototype prot. gene, upper estimation |
| DNA_identity | Identity between prototype gene and pseudogene at the level of DNA |
| CDS length | (nt.) CDS length |