The pairwise alignment has been generated with the "genewise" program of the Wise2 package. The output shows the protein sequence on the first line, followed by a line indicating the similarity level of the match, followed by 4 lines representing the DNA sequence; The DNA sequence descending in triplets, each triplet being a codon. The translation of each codon is shown above it.
Between the two protein sequences a line indicating the similarity of the match is printed. "+" indicates a conservative mismatch while "- "indicates a dramatic one. Mismatches are indicated by "***" in the left column in addition to "!" at the relevant position(s).
genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright
Query protein: RNQ1_YEAST
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AY028681_4
Strand: forward
Start/End (protein) default
Gene Paras: human.gf
Codon Table: codon.table
Subs error: 1e-05
Indel error: 1e-05
Model splice? model
Model codon bias? flat
Model intron bias? tied
Null model syn
Algorithm 623
genewise output
Score 578.47 bits over entire alignment
Scores as bits over a synchronous coding model
Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info.
Warning: protein length=405 (x3=1215) and cDNA length=808
Warning: mismatch(es) found
RNQ1_YEAST 138 LAALASQFFKSGNNSQGQGQGQGQGQGQGQGQGQGSFTALASLASSFMN
LAALASQFFKSGNNSQGQGQGQGQGQGQGQGQG--SFTALASLASSFMN
LAALASQFFKSGNNSQGQGQGQGQGQGQGQGQG--SFTALASLASSFMN
AY028681_4 2 cggtgtcttatgaatcgcgcgcgcgcgcgcgcg ttagtgttgtttaa
tcctccattacgaacagagagagagagagagag ctcctcctccctta
gtcgttactgatctcatgaatatataaatatat ttttggtgtatcgt
*** !!
RNQ1_YEAST 187 SNNNNQQGQNQSSGGSSFGALASMASSFMHSNNNQNSNNSQQGYNQSYQ
SNNNNQQGQNQSSGGSSFGALASMASSFMHSNNNQNSNNSQQGYNQSYQ
SNNNNQQGQNQSSGGSSFGALASMASSFMHSNNNQNSNNSQQGYNQSYQ
AY028681_4 143 taaaaccgcacatggtttggcgtagattactaaacataaaccgtacttc
caaaaaagaaagcggcctgctcctcgcttacaaaaacaagaagaaacaa
cccttgatataccttcctaagttgacttgtctttgcccttagttcacta
RNQ1_YEAST 236 NGNQNSQGYNNQQYQGGNGGYQQQQGQSGGAFSSLASMAQSYLGGGQTQ
NGNQNSQGYNNQQYQGGNGGYQQQQGQSGGAFSSLASMAQSYLGGGQTQ
NGNQNSQGYNNQQYQGGNGGYQQQQGQSGGAFSSLASMAQSYLGGGQTQ
AY028681_4 290 agacaacgtaacctcggaggtccccgctgggttttgtagctttgggcac
agaaagagaaaaaaaggaggaaaaagacggctcctcctcacatgggaca
ctcattatcttagcatccttcaaagaatttttcagccgtatcattaata
RNQ1_YEAST 285 SNQQQYNQQGQNNQQQYQQQGQNYQHQQQGQQQQQGHSSSFSALASMAS
SNQQQY-----------QQQGQNYQHQQQGQQQQQGHSSSFSALASMAS
SNQQQY-----------QQQGQNYQHQQQGQQQQQGHSSSFSALASMAS
AY028681_4 437 taccct cccgcatcccccgcccccgctatttgtgtaga
caaaaa aaagaaaaaaaagaaaaagacgctcctcctcg
ccggac gaacactgcaagtgggaaccctacatgtcgat
*** !!!!!!!!!!!
RNQ1_YEAST 334 SYLGNNSNSNSSYGGQQQANEYGRPQQNGQQQSNEYGRPQ---------
SYLGNNSNSNSSYGGQQQANEYGRPQ-NGQQQSNEYGRPQ
SYLGNNSNSNSSYGGQQQANEYGRPQHNGQQQSNEYGRPQHNGQQQSNE
AY028681_4 551 ttcgaatatatatggcccgagtgacccagccctagtgacccagccctag
catgaacacacgaggaaacaaaggcaaagaaacaaaggcaaagaaacaa
ccgctcctatgttgcgagttgttaaacttaaattgcaagacttagattg
*** !
RNQ1_YEAST 374 -----YGGNQNSNGQHESFNFSGNFSQQNNNGNQNRY
-----YGGNQNSNG-HESFNFSGNFSQQNNNGNQNRY
YGRPQYGGNQNSNGHHESFNFSGNFSQQNNNGNQNRY
AY028681_4 698 tgacctggacatagccgttattgattccaaagacact
aggcaaggaaacagaaactatcgatcaaaaagaaaga
caagaccacgcctaccacctttccttagctcccgccc
*** !!!!! !
//
cmbi.ru.nl), 18-Aug-2005