WISE2

Algoritmos inteligentes para busca em DNA

http://www.sanger.ac.uk/Software/Wise2/

O que é o WISE2 ?

Wise2 é um pacote orientado à comparação de seqüências de DNA ao nível de tradução, desprezando erros de seqüenciamento e Introns.

Wise2 é um pacote orientado à comparação de biopolímeros, comumente seqüências de DNA e proteínas.

Tradução

Processo pelo qual a informação genética ( que é estocada na seqüência de nucleotídeos numa molécula de mRNA) é traduzida em uma seqüência de aminoácidos

Exon-GU..............................................AG-ExonIntron

DNA Exon 1 Intron A Exon 2 Intron B Exon 3

transcrição

Transcrito 5’ Exon 1 Intron A Exon 2 Intron B Exon 3 3’

Primário: Códon n Códon n+1 ---------------------

Processamento do RNA

mRNA Exon 1 Exon 2 Exon 3 --

tradução

Polipeptídeo

Concorrentes:

•BLAST package ( NCBI) Sequence Searching

•Fasta package (Bill Pearson) Sequence Searching

•SAM package (UC Santa Cruz) HMM

•HMMER package (Sean Eddy) HMM

Os HMMER e Pfam podem ser classificados como parceiros !!

•O ponto forte do Wise2 é a comparação de seqüência de DNA a nível de sua tradução protéica .

•Implementação dos algoritmos mais robusta:

•Integração tecnológica faz do WISE2 o parceiro ideal para o HMMER e Pfam;

•Design permite reutilização e alteração do código.

Quais as vantagens do WISE2?

Manuseio de grandes pedaços de DNA sem estouro de memória;

Desvantagens

• O algoritmo GENEWISE não tenta predizer um gene inteiro, mas regiões que apresentam homologia com a proteína. - porém é confiável!

•Velocidade (Maior preocupação com a algoritmos corretos que com velocidade) Opções -u -v ( início e final de cadeia de DNA a ser comparada) Scripts em Pearl - Blastwise e Halfwise

• Até o momento dispõe somente de arquivos de freqüencia de genes em Humanos e Vermes.

• Uso de memória Linear com perda de desempenho quando uso de matrizes ultrapassam 20 MB

Modos4 programas principais executáveis:

• Genewise

Cadeia proteica vs Seqüência simples de DNA • Genewisedb

Banco de dados de proteínas vs banco de dados de seqüências de DNA.

• Estwise

Cadeia proteica vs Seqüência simples de cDNA/EST• Estwisedb

Banco de dados de proteínas vs banco de dados de seqüências de cDNA/EST.

-u Posição inicial no DNA-v Posição final no DNA-trev Comparação do reverso -tfor (default) Comparação standard -both Comparação nos dois sentidos-s Posição inicial na proteína - não aplicável a HMM-t Posição final na proteína - não aplicável a HMM -gap [no] default [12] gap penalty -ext [no] default [2] extension penalty -matrix default [blosum62.bla] Matriz de Comparação. Estima a probabilidade de comparações de aminoácidos -hmmer especifica que o modelo proteico é do tipo HMM -hname Nomeia o HMM -init DEFAULT

OPÇÕES

genewise protein.pep cosmid.dna compara uma seqüência proteica a uma de DNA genewise -hmmer pkinase.hmm cosmid.dna compara uma seqüência proteica ( HMM) a uma de DNA .

GENEWISE

genewisedb protein.pep human.fa compara uma seqüência proteica a um banco de DNA

genewisedb -hmmer pkinase.hmm human.fa compara uma seqüência proteica (HMM) a um banco de DNA

genewisedb -prodb protein.pep -dnas cosmid.dna compara um banco de seqüências proteicas a uma seqüência de DNA

genewisedb -pfam Pfam -dnas cosmid.dna compara um banco de seqüências proteicas (HMM) a uma seqüência de DNA

genewisedb -prodb protein.pep human.fa compara um banco de seqüências proteicas a um de seqüências de DNA

genewisedb -pfam Pfam human.fa compara um banco de seqüências proteicas (HMM) a uma seqüência proteica

GENEWISEdb

ESTWISE

estwise protein.pep singleest.fa compara uma seqüência proteica a uma de DNA

estwise -hmmer pkinase.hmm singleest.fa compara uma seqüência proteica (HMM) a uma de DNA

estwisedb protein.pep est.fa compara uma seqüência proteica a um banco de DNA

estwisedb -hmmer pkinase.hmm est.fa compara uma seqüência proteica (HMM) a um banco de DNA

estwisedb -prodb protein.pep -dnas singleest.fa compara um banco de seqüências proteicas a uma de DNA

estwisedb -pfam Pfam -dnas singleest.fa compara um banco de seqüências proteicas (HMM) a uma de DNA

estwisedb -prodb protein.pep est.fa compara um banco de seqüências proteicas a um banco de DNA

ESTWISEdb

Genewise example

•Usage •genewise <protein-file> <dna-file> in fasta format

Options. In any order, '-' as filename (for any input) means stdin Dna [-u,-v,-trev,-tabs,-fembl,-both] Protein [-s,-t,-g,-e,-m] HMM [-hmmer,-hname] Model [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null] Alg [-kbyte,-alg] Output [-pretty,-genes,-para,-sum,-cdna,-trans,-ace,-embl,-diana] ..cont [-gff,-gener,-alb,-pal,-block,-divide] Standard [-help,-version,-silent,-quiet,-errorlog]

roa1_drome 187 LNGKMVDVKKALPKQNDQQGGGGGR +NG +V+KAL KQ R VNGHNCEVRKALSKQEMASASSSQR G:G[ggt] HSHNRNPA 2405 gagcatggaagctacgagagttacaGGTATGCT Intron 4 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793] gtccctataacgagaggtttaccaa

Genewisedb

genewisedb road.pep hngen.fa

Query protein: roa1_dromeComp Matrix: blosum62.blaGap open: 12Gap extension: 2Start/End localTarget Sequence HSHNRNPAStrand: forwardGene Paras: human.gfCodon Table: codon.tableSubs error: 1e-05Indel error: 1e-05Model splice? modelModel codon bias? flatModel intron bias? tiedNull model synAlgorithm 623Find start end points: [25,1387][346,3962] Score 87719Recovering alignment: Alignment recoveredExplicit read offone 94%genewise outputScore 253.10 bits over entire alignmentScores as bits over a synchronous coding model

Warning: The bits scores is not probablistically correct for single seqsSee WWW help for more info

Ex 1

genewise fly.pep human.genomic > genewise.out

>ROA1_DROME P07909 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HNRNP CORE PROTEIN A1-A) (PEN REPEAT CLONE P9).

MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDINIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKQNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGGNNQGFNNGGNNRRY

fly.pep

>HSHNRNP

ACGCAAAGCTAGGACAAACTCCCGCCAACACGCAGGCGCCGTAGGTTCACTGCCTACTCCTGCCCGCCATTTCACGTGTTCTCAGAGGCAGGTGGAACTTCTTAATGCGCCTGCGCAAAACTCGCCATTTTACTACACGTGCGGTCAACAAGAGTTCATTGCAAAAAAATTGTTACCTCCTAGCTGCTTGTCTAATACATAGTGTTAATCATGCTTTGCCAAGCGACTTGACTGTAATATTTGCGCGTGGAAGATTAAAAAGATGTTAAACACCCAAGGTAGATTCAAATGTGAATGATTGGTCGGTTGGCCAATCAGACTGGTTAACAATAACATTACTCGGGAACCAATGGACTCCAAGGGGTGGAGACGGCGTAGAACGACCGAAGGAATGACGTTACACAGCAATGTGGCACCACAGGCCAATAGCAGGGGGAAGCGATTTCAAGTATCCAATCAGAGCTGTTCTAGGGCGGAGTCTACCAATGCCGAAAGCGAGGAGGCGGGGTAAAAAAGAGAGGGCGAAGGTAGGCTGGCAGATACGTTCGTCAGCTTGCTCCTTTCTGCCCGTGGACGCCGCCGAAGAAGCATCGTTAAAGTCTCTCTTCACCCTGCCGTCATGTCTAAGTCAGAGGTGAGTTAGGCGCGCTTTCCCACTTGAATTTTTTCCTCTCCCTTTCCTGAATCGGTAAGATGCTGCTGGGTTTCGTTCCTTGCACCAGCCCATTCTACAGTTCCTTCGGTCGCTGCCACGGCCTACCCCTCCCAAAGTTCAAGTCGCCATTTTGTCCTCTTGATCGCCATGAGGCCGCTCTCCGCCAACCATGTGTTATCATGCGGGACTCGTTACTCGTAGCAAAATTCTTAGGCACACAGGATCTTTGTCTTTTTTTAAACCTTGCCTTGGTGAGCGAGTTTTCTAAAGAGCGATTAGTCCCATTGTGGAGATGCACCCCTACCGCCCAAGCCTTTGTTGCGCGTGCGTCGGAAGGCGACTAGGGACGCATGCGCTTGCGATTTCCTAGCACTCCCAACTCCAGCATACGGCCTCCCTTGATAGGCAGAAGCACGTGTCTTGTTGCGACCTGAACGAACAATAAGTGCTAGGTACACAGTTGGTGTCTAGTTTTTCTTTTCCTCGATGGAAATTGTTTCGTGTTGTAGCCCATTTAACACTTCCCCCTCCCCCCACTCTAGTCTCCTAAAGAGCCCGAACAGCTGAGGAAGCTCTTCATTGGAGGGTTGAGCTTTGAAACAACTGATGAGAGCCTGAGGAGCCATTTTGAGCAATGGGGAACGCTCACGGACTGTGTGGTAAGATTTGGAAGGGACAAAGCAGTAAAACAGCCGATTTCCTTGGCTTATCTTGGTGCAGTCTTCTCCGAATGCTTATGAAAGTAGTTAATAGCATTATAGTTAGAGCTTTGTTGGCAAAGGAACGTCCTGCTTTGATTTTAAAAGCTAACCTCTTAAATCTAAGGGTAGTGGGAAACTGGACGAACTTTTTATAAAAGGCTGGTGTAAAGTTTCCTATTGCCCTATTCAAAGTTAAAATAACAAAAGCTTTTGCGGTCAGACTTTGTGTTACATAAATTAACACTGTTCTCAGGTAATGAGAGATCCAAACACCAAGCGCTCTAGGGGCTTTGGGTTTGTCACATATGCCACTGTGGAGGAGGTGGATGCAGCTATGAATGCAAGGCCACACAAGGTGGATGGAAGAGTTGTGGAACCAAAGAGAGCTGTCTCCAGAGAAGTGAGTGGGTTTTTTTTCTTCTTCTTCTTAAACTTACTTGGATATGTGCTGCTATGAACTTAAGATTCGGGAGTTTTCTAAACTTACCAAAATTTTTTATTCGAGTATAGGCTTTGCTAATCTAAACCTATGGTTTTTCTCCTATTAGGATTCTCAAAGACCAGGTGCCCACTTAACTGTGAAAAAGATATTTGTTGGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGACTGACCGAGGCAGTGGCAAGAAAAGGGGCTTTGCCTTTGTAACCTTTGACGACCATGACTCCGTGGATAAGATTGTCAGTAAGTATCAGATAGTGGCATTTAGTAAGGGTTCCACAATCTGTATGGCATTCTAAACCCTGATACCATGTTGTATCTATGTTTTTTTTTTAGTTCAGAAATACCATACTGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTCAAAGCAAGAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTATGCTTGTTGCTTAATTAAACCTTAAAGGTAACTTTGAGTTACTCCAGTATGAATGATTTAATGCTTAAACTTCATGTCTTAAGGTCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTCGGTGGGAATGACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTGGTATGTATGGTTTATCTACATGTAGTTCTGACTTCTCACCATCTTTGCTATGAAGATTTTACAGTACGGGAACTGCATTCAGAATGTCACTTTAAGTCCAAGTCATACTTAAAACTTGAAACTTTTTCTTACAGGTGGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGTGGCAGTGGGGATGGCTATAATGGATTTGGCAATGATGGTAAGTTTTTTAGGAATAAGTAGAGAAAAATTCCTGGCAACCTGGATCTTTAGAATAGGTTAGTAGAGACTAAAATTCTGGTGCATGTCAAACTCAACTTTGCCCATAACACGCATGCTGTGAGCAGGCCTTCAGCCGTTACACTTGCACAAGTTTTCATTGTCAAATACTTTTGTCTTATTGAGAAGAATTGTATTCTTGTAGGTGGTTATGGAGGAGGCGGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGAAGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGCGGGAGTGGCAGCTATGACAGCTATAACAACGGAGGCGGAGGCGGCTTTGGCGGTGGTAGTGGTAGGTATCCAGTGATCCAAGTACTTGGTGTGACAGCTAGATTAGCCTTTTAGAGCTTGGGTTCTGGTGCTGTTGAAGCATTGTGTGGTACACTGCATGGTATATTAAAAACAAATGGGCTTGCTATGCTACCTCCTCCTAGCTTTAAGCTGGGGCCGCCTCACTCCCAAATAGTAGAGATAAGTGGATAGTGTTGTCTTTGAGTTAGATTAGTATCATAGAAGGATTTAGTATTTTAACTCCTTTGGGACCTTAGGCGCTTAGTTGATGTATCCAAGATACTTCTGCTTGCTGTGGCCCTGGATCCGTGAAGGCCTTCAAGGCTGAAGGGTATGCTTGTGCCACTCTGAAAATCTCTTTATTTTATGTCATGGTGAGTTAGGCCAGTTTTCTTTGTATTACTGGATTATTCAACTGAATGCCTTTCCCAGAGAATGAAATGCAAAGATTGGAGTCACCATAGTTTGGGAGAAAGGAAGGCTGATAACTCAACCTTATTTTATTCTGACTGCTAAACAGAATTGGAAACTAACATCATCCTCAGGTAACAGATAAAGGCCCTCTTTCCCATTCATAGGAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATTACAACAATCAGTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGGAGGCAGAAGCTCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAACCACGAAACCAAGGTATGGTATCTATGTAATTTTGGATAATGTCAAAAGAGTGTCTGTAGCTACTGCTGGGAAGAAAGCCCTTTAACTGCTATGTCTGGGCAGCAAAACGTTTATAGTTTAGAACCTTCAGAAAGTGATAATTTGATCACAAATTAGAAAAATCATGGGACCTCTTTACCACCTCCCTTGTAGTAGGGCCATTTTTAAATGGCCAGACACTTGAATTTAACTTTTATTATCCCAAATATGAAAACATTACTGTTGGCACTTTGAAACTTTAAAAGAAAAATTGTACTTTTCAGGTGGCTATGGCGGTTCCAGCAGCAGCAGTAGCTATGGCAGTGGCAGAAGATTTTAATTAGGTAAGTAAGCACCTTTTTGTGTGTTGACATAATTTTTTAAATTGCTGATGAACCCAATAACCCTAATGTAGCTGAGCAGTGCAACATAGTTAACATTATAATTGCAGTAATTGTGGATATAAAGTTAATATTCAGATCAGCAAAATTTGTGGGAAACAAACTTGATATTGGATTGTAGCCTTGAGTCTTAATATGTTTAGATTAACAACTCTATTCCATATTGTTCAACAGGAAACAAAGCTTAGCAGGAGAGGAGAGCCAGAGAAGTGACAGGGAAGCTACAGGTTACAACAGATTTGTGAACTCAGC

human.genomic

genewise fly.pep human.genomic > genewise.out

Query protein: ROA1_DROMEComp Matrix: blosum62.blaGap open: 12Gap extension: 2Start/End defaultTarget Sequence HSHNRNPAStrand: forwardStart/End (protein) defaultGene Paras: human.gfCodon Table: codon.tableSubs error: 1e-05Indel error: 1e-05Model splice? modelModel codon bias? flatModel intron bias? tiedNull model synAlgorithm 623

genewise outputScore 253.10 bits over entire alignmentScores as bits over a synchronous coding model

Warning: The bits scores is not probablistically correct for single seqs

genewise.out

ROA1_DROME 26 EPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDVV EPE +RKLFIGGL + TTDE+L++HFE+WG + D V EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV HSHNRNPA 1206 gcgccaactaggtatgaaggacaactgctgacagtg acaatgatttggtgtaccaagtggataaggctcagt gcaggggcctaggctaattgcggcttgagagcgctg

ROA1_DROME 62 VMKDPRTKRSRGFGFITYSHSSMIDE VM+DP TKRSRGFGF+TY+ +D VMRDPNTKRSRGFGFVTYATVEEVDA HSHNRNPA 1314 GTAAGAT Intron 1 CAGgaagcaaactagtgtgatgagggggg <0-----[1314 : 1608]-0>ttgacacagcggtgttcacctaatac agataccgctgctgtcatctggggta

ROA1_DROME 88 AQKSRPHKIDGRVVEPKRAVPRQ DID A +RPHK+DGRVVEPKRAV R+ D AMNARPHKVDGRVVEPKRAVSRE DSQ HSHNRNPA 1687 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc ctacgcaataggttacagctcga<0-----[1756 : 1903]-0>aca tgtagacggtaatgaagatccaa tta

ROA1_DROME 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDINIVIDKETGKK P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK HSHNRNPA 1913 acggctagaaatgggaaggaggcccagttgctgaaggagaaagcgagaa gcgcatctaatttggtaaacaaaatgaataaagatattattcaggggaa aatccatgagatttctaactaatcaatttagtaatagtacgtcactcga

Alignment 1 Score 35.31 (Bits)

SEED 1 CAPNN-PCSNGGTCVNTPGGSSDNFGGYTCECPPGDYYLSYTGKRC CA++ C++ +CVN + +++C+C PG Y L+ + K C CAEGGHGCQH--QCVNAWA-------MFHCTCNPG-YKLAADNKSC EM:HS453C12 132851 tggggcgtcc ctgagtg atctatacg tacgggaaat gcaggaggaa agtacgc ttagcgacg aatccaaagg ttggattcgc atctcgc gccccccac CGAAATCGCT

Alignment 2 Score 45.92 (Bits)

SEED 1 CAPNN-PCSNGGTCVNTPGGSSDNFGGYTCECPPGDYYLSYTGKRC CA+++ C + CVN+PG +Y+C+C++G +L+ + + C CAEGTHGCEH--HCVNSPG-------SYFCHCQVG-FVLQQDQRSC EM:HS453C12 134919 tgggacgtgc ctgatcg ttttctcgg tgcccgcaat gcagcaggaa agtaccg catgagatg tttaaaaggg ttagctatgc ccctcac ctctccatc tacggcggcc

Ex 2

tggcatggggcgcaggttctctatacaccccccgcccccggctgccaggctctgcggcctcaccttggaactacagggcaagagcttcttccagggggtgaggttttcggtgcagaccacctcccgcggcagcacagcatagcgcagaaagtagtggtcagtgtctgagggagacagaggtctgtctggggtgggccttgggctctgacccctcgggatccacattccagagatgggaatgaccctcctgctccccacaccacctctagcaccacagtctggacagtcccaactgggagtaggactcccttctctccttgggaaaaggcatgcagagatggcacagtattgggggcctgcacacacaggggacttaggatctagcccaggctgaggaagcaggaaactgagggaaaaggaggcaaaggtttgggcaggaggtaagaggaagaaggaaagggctgtaggggttatctcaccattggccagacccaggggtttgaaggaggcagtgggagtgactgtgttggtggagtcgatgaagttgagagaggcgcagaagatccctgagaggacattactgagctccttccaagatttatccacactggatagagacacaaatccactcactgtcctggggctacctctgctccctctttcaaagtccacagctggctgctaaacctatgataggaggaggctgtattcttaactattagacgggccagttgatggagctggaacattgctgcccccagccagcccacttgctgggtctcatcctactcagccccttcttcctcactctcctctggacatctctgcatccccatgggtctctgctcaggtgattcttccttccttgcaagcctttgctaacttctttctgcctaccttcatgatccggctccagtgcttacctcccctccacgaagcctttcctgccctccttaagcacagtctcctctgtgcagtcacggttctgaccatccaagcatcttactaggtccctcctgggagatggctaggtggcagcagcatcgtgtcctgaccaccttttctccctaactaggctgtaagcaacttgaggacaaggaccagtctgggtcatctatgtacttcccctgacaccatggaaagcgcctcatgtatcagagctgaaatgagctcactgatcttccttgaatgtgctgggctgggcaaaacaatgcatactaccctgtgtatactctgggaataaaggtaagtcctgattctactatcatggtgagaagtcttatatccaaaaaagctcactgaacatgggaaaaacaactgttctaggatttcataaaaacatcaaattaaattaatgttcttttcttggagaaatatcaaaagagatttgctctcagtaatagagaaagcataaaacttaataagcactagaaagaattctaagcatttgctccacatttcaggcaattacgggctgagggaagacagtgacagcagagtagacaggaaagggtaggggagccagagttgaggcaagagagaaagtcttggcaagctggggagttactgcttattccttattccttagtgttgtccaggagcttttgataattctatgttcagagcttttcaactgctccaatccttaagcctcaaataaaaatggcaaacttgaagccggaaagctctactcaaaccataaacatgcttcatttggtatgcacaacattgacccgcacagcactcaaaaaatttttaaattacttgctgatatttgaatttgccaattttcacattaaattccagatttctggtatctcttgaaaaatgaggccaggtgtggtggctcttgcctgtaatcccaacactttgggaggctgaggcaggaggatCGCTtgaacccaggagttcgagaccagcctgggcaatatagtgagaccttgtttctacaaaaaatttttagaaacatttgactctgaccacattaggcctctattcccacatggcaacaatccatagaagctgagtggcagagctgtcctcg