NucleaRDB: Pairwise Alignments

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:       THB2_HUMAN
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            default
Target Sequence      HSTHRBI_3
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 319.34 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=476 (x3=1428) and cDNA length=366

THB2_HUMAN         1 MNYCMQEIYEVHPAAGSNCYMQSTDYYAYFEDSPGYSGCDAQAVPSNNI 
                     MNYCMQEIYEVHPAAGSNCYMQSTDYYAYFEDSPGYSGCDAQAVPSNNI 
                     MNYCMQEIYEVHPAAGSNCYMQSTDYYAYFEDSPGYSGCDAQAVPSNNI 
HSTHRBI_3          1 aattacgatggccgggaattactagttgttggacgtagtggcggcaaaa 
                     taagtaataatacccggagataccaaacataagcgagggacactcgaat 
                     gcctgaaatagcatccctccggctttcgttattgtccttttgtgctcca 


THB2_HUMAN        50 YMEQAWAVNQPYTCSYPGNMFKSKDSDLDMALNQYSQPEYFTEEKPTFS 
                     YMEQAWAVNQPYTCSYPGNMFKSKDSDLDMALNQYSQPEYFTEEKPTFS 
                     YMEQAWAVNQPYTCSYPGNMFKSKDSDLDMALNQYSQPEYFTEEKPTFS 
HSTHRBI_3        148 tagcgtggacctatatcgaataaagtgtgagcactaccgttaggacatt 
                     ataacgctaacacggacgattagaacatatctaaagacaatcaaacctc 
                     tgagcgagtgttcttctacgtacgctcgcgcgtaccatatctaagtttt 


THB2_HUMAN        99 QVQSPSYSQKKGYIPSYLDKDELC                          
                     QVQSPSYSQKKGYIPSYLDKDELC                          
                     QVQSPSYSQKKGYIPSYLDKDELC                          
HSTHRBI_3        295 cgctctttcaagtacattgaggct                          
                     atacccacaaagatcgataaaatg                          
                     agggagttaaagccctcacgcgct                          


//

F.Horn (nucleardbcmbi.kun.nl), 18-Feb-2005