WISE2 Algoritmos inteligentes para busca em DNA

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1 WISE2 Algoritmos inteligentes para busca em DNA

2 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.

3 DNA Exon 1 Intron A Exon 2 Intron B Exon 3 transcrição 
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 Intron Exon-GU AG-Exon DNA Exon Intron A Exon Intron B Exon 3 transcrição  Transcrito ’ Exon 1 Intron A Exon Intron B Exon 3 3’ Primário: Códon n Códon n Processamento do RNA  mRNA Exon 1 Exon 2 Exon tradução  Polipeptídeo

4

5 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 !!

6 Quais as vantagens do WISE2?
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. Manuseio de grandes pedaços de DNA sem estouro de memória;

7 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

8 Modos 4 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.

9 OPÇÕES -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

10 GENEWISE 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 .

11 GENEWISEdb 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

12 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

13 ESTWISEdb 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

14 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]

15 genewisedb road.pep hngen.fa
Query protein: roa1_drome Comp Matrix: blosum62.bla Gap open: Gap extension: Start/End local Target Sequence HSHNRNPA Strand: forward Gene Paras: human.gf Codon Table: codon.table Subs error: e-05 Indel error: e-05 Model splice? model Model codon bias? flat Model intron bias? tied Null model syn Algorithm Find start end points: [25,1387][346,3962] Score 87719 Recovering alignment: Alignment recoveredExplicit read offone 94% genewise output Score 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 Genewisedb genewisedb road.pep hngen.fa Ex 1 roa1_drome LNGKMVDVKKALPKQNDQQGGGGGR +NG +V+KAL KQ R VNGHNCEVRKALSKQEMASASSSQR G:G[ggt] HSHNRNPA gagcatggaagctacgagagttacaGGTATGCT Intron 4 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793] gtccctataacgagaggtttaccaa

16 genewise fly.pep human.genomic > genewise.out
>ROA1_DROME P07909 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HNRNP CORE PROTEIN A1-A) (PEN REPEAT CLONE P9). MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDINIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKQNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGGNNQGFNNGGNNRRY

17 genewise fly.pep human.genomic > genewise.out
>HSHNRNP ACGCAAAGCTAGGACAAACTCCCGCCAACACGCAGGCGCCGTAGGTTCACTGCCTACTCCTGCCCGCCATTTCACGTGTTCTCAGAGGCAGGTGGAACTTCTTAATGCGCCTGCGCAAAACTCGCCATTTTACTACACGTGCGGTCAACAAGAGTTCATTGCAAAAAAATTGTTACCTCCTAGCTGCTTGTCTAATACATAGTGTTAATCATGCTTTGCCAAGCGACTTGACTGTAATATTTGCGCGTGGAAGATTAAAAAGATGTTAAACACCCAAGGTAGATTCAAATGTGAATGATTGGTCGGTTGGCCAATCAGACTGGTTAACAATAACATTACTCGGGAACCAATGGACTCCAAGGGGTGGAGACGGCGTAGAACGACCGAAGGAATGACGTTACACAGCAATGTGGCACCACAGGCCAATAGCAGGGGGAAGCGATTTCAAGTATCCAATCAGAGCTGTTCTAGGGCGGAGTCTACCAATGCCGAAAGCGAGGAGGCGGGGTAAAAAAGAGAGGGCGAAGGTAGGCTGGCAGATACGTTCGTCAGCTTGCTCCTTTCTGCCCGTGGACGCCGCCGAAGAAGCATCGTTAAAGTCTCTCTTCACCCTGCCGTCATGTCTAAGTCAGAGGTGAGTTAGGCGCGCTTTCCCACTTGAATTTTTTCCTCTCCCTTTCCTGAATCGGTAAGATGCTGCTGGGTTTCGTTCCTTGCACCAGCCCATTCTACAGTTCCTTCGGTCGCTGCCACGGCCTACCCCTCCCAAAGTTCAAGTCGCCATTTTGTCCTCTTGATCGCCATGAGGCCGCTCTCCGCCAACCATGTGTTATCATGCGGGACTCGTTACTCGTAGCAAAATTCTTAGGCACACAGGATCTTTGTCTTTTTTTAAACCTTGCCTTGGTGAGCGAGTTTTCTAAAGAGCGATTAGTCCCATTGTGGAGATGCACCCCTACCGCCCAAGCCTTTGTTGCGCGTGCGTCGGAAGGCGACTAGGGACGCATGCGCTTGCGATTTCCTAGCACTCCCAACTCCAGCATACGGCCTCCCTTGATAGGCAGAAGCACGTGTCTTGTTGCGACCTGAACGAACAATAAGTGCTAGGTACACAGTTGGTGTCTAGTTTTTCTTTTCCTCGATGGAAATTGTTTCGTGTTGTAGCCCATTTAACACTTCCCCCTCCCCCCACTCTAGTCTCCTAAAGAGCCCGAACAGCTGAGGAAGCTCTTCATTGGAGGGTTGAGCTTTGAAACAACTGATGAGAGCCTGAGGAGCCATTTTGAGCAATGGGGAACGCTCACGGACTGTGTGGTAAGATTTGGAAGGGACAAAGCAGTAAAACAGCCGATTTCCTTGGCTTATCTTGGTGCAGTCTTCTCCGAATGCTTATGAAAGTAGTTAATAGCATTATAGTTAGAGCTTTGTTGGCAAAGGAACGTCCTGCTTTGATTTTAAAAGCTAACCTCTTAAATCTAAGGGTAGTGGGAAACTGGACGAACTTTTTATAAAAGGCTGGTGTAAAGTTTCCTATTGCCCTATTCAAAGTTAAAATAACAAAAGCTTTTGCGGTCAGACTTTGTGTTACATAAATTAACACTGTTCTCAGGTAATGAGAGATCCAAACACCAAGCGCTCTAGGGGCTTTGGGTTTGTCACATATGCCACTGTGGAGGAGGTGGATGCAGCTATGAATGCAAGGCCACACAAGGTGGATGGAAGAGTTGTGGAACCAAAGAGAGCTGTCTCCAGAGAAGTGAGTGGGTTTTTTTTCTTCTTCTTCTTAAACTTACTTGGATATGTGCTGCTATGAACTTAAGATTCGGGAGTTTTCTAAACTTACCAAAATTTTTTATTCGAGTATAGGCTTTGCTAATCTAAACCTATGGTTTTTCTCCTATTAGGATTCTCAAAGACCAGGTGCCCACTTAACTGTGAAAAAGATATTTGTTGGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGACTGACCGAGGCAGTGGCAAGAAAAGGGGCTTTGCCTTTGTAACCTTTGACGACCATGACTCCGTGGATAAGATTGTCAGTAAGTATCAGATAGTGGCATTTAGTAAGGGTTCCACAATCTGTATGGCATTCTAAACCCTGATACCATGTTGTATCTATGTTTTTTTTTTAGTTCAGAAATACCATACTGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTCAAAGCAAGAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTATGCTTGTTGCTTAATTAAACCTTAAAGGTAACTTTGAGTTACTCCAGTATGAATGATTTAATGCTTAAACTTCATGTCTTAAGGTCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTCGGTGGGAATGACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTGGTATGTATGGTTTATCTACATGTAGTTCTGACTTCTCACCATCTTTGCTATGAAGATTTTACAGTACGGGAACTGCATTCAGAATGTCACTTTAAGTCCAAGTCATACTTAAAACTTGAAACTTTTTCTTACAGGTGGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGTGGCAGTGGGGATGGCTATAATGGATTTGGCAATGATGGTAAGTTTTTTAGGAATAAGTAGAGAAAAATTCCTGGCAACCTGGATCTTTAGAATAGGTTAGTAGAGACTAAAATTCTGGTGCATGTCAAACTCAACTTTGCCCATAACACGCATGCTGTGAGCAGGCCTTCAGCCGTTACACTTGCACAAGTTTTCATTGTCAAATACTTTTGTCTTATTGAGAAGAATTGTATTCTTGTAGGTGGTTATGGAGGAGGCGGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGAAGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGCGGGAGTGGCAGCTATGACAGCTATAACAACGGAGGCGGAGGCGGCTTTGGCGGTGGTAGTGGTAGGTATCCAGTGATCCAAGTACTTGGTGTGACAGCTAGATTAGCCTTTTAGAGCTTGGGTTCTGGTGCTGTTGAAGCATTGTGTGGTACACTGCATGGTATATTAAAAACAAATGGGCTTGCTATGCTACCTCCTCCTAGCTTTAAGCTGGGGCCGCCTCACTCCCAAATAGTAGAGATAAGTGGATAGTGTTGTCTTTGAGTTAGATTAGTATCATAGAAGGATTTAGTATTTTAACTCCTTTGGGACCTTAGGCGCTTAGTTGATGTATCCAAGATACTTCTGCTTGCTGTGGCCCTGGATCCGTGAAGGCCTTCAAGGCTGAAGGGTATGCTTGTGCCACTCTGAAAATCTCTTTATTTTATGTCATGGTGAGTTAGGCCAGTTTTCTTTGTATTACTGGATTATTCAACTGAATGCCTTTCCCAGAGAATGAAATGCAAAGATTGGAGTCACCATAGTTTGGGAGAAAGGAAGGCTGATAACTCAACCTTATTTTATTCTGACTGCTAAACAGAATTGGAAACTAACATCATCCTCAGGTAACAGATAAAGGCCCTCTTTCCCATTCATAGGAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATTACAACAATCAGTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGGAGGCAGAAGCTCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAACCACGAAACCAAGGTATGGTATCTATGTAATTTTGGATAATGTCAAAAGAGTGTCTGTAGCTACTGCTGGGAAGAAAGCCCTTTAACTGCTATGTCTGGGCAGCAAAACGTTTATAGTTTAGAACCTTCAGAAAGTGATAATTTGATCACAAATTAGAAAAATCATGGGACCTCTTTACCACCTCCCTTGTAGTAGGGCCATTTTTAAATGGCCAGACACTTGAATTTAACTTTTATTATCCCAAATATGAAAACATTACTGTTGGCACTTTGAAACTTTAAAAGAAAAATTGTACTTTTCAGGTGGCTATGGCGGTTCCAGCAGCAGCAGTAGCTATGGCAGTGGCAGAAGATTTTAATTAGGTAAGTAAGCACCTTTTTGTGTGTTGACATAATTTTTTAAATTGCTGATGAACCCAATAACCCTAATGTAGCTGAGCAGTGCAACATAGTTAACATTATAATTGCAGTAATTGTGGATATAAAGTTAATATTCAGATCAGCAAAATTTGTGGGAAACAAACTTGATATTGGATTGTAGCCTTGAGTCTTAATATGTTTAGATTAACAACTCTATTCCATATTGTTCAACAGGAAACAAAGCTTAGCAGGAGAGGAGAGCCAGAGAAGTGACAGGGAAGCTACAGGTTACAACAGATTTGTGAACTCAGC

18 genewise.out Query protein: ROA1_DROME Comp Matrix: blosum62.bla
Gap open: Gap extension: Start/End default Target Sequence HSHNRNPA Strand: forward Start/End (protein) default Gene Paras: human.gf Codon Table: codon.table Subs error: e-05 Indel error: e-05 Model splice? model Model codon bias? flat Model intron bias? tied Null model syn Algorithm genewise output Score bits over entire alignment Scores as bits over a synchronous coding model Warning: The bits scores is not probablistically correct for single seqs genewise.out

19 ROA1_DROME 26 EPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDVV
EPE +RKLFIGGL + TTDE+L++HFE+WG + D V EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV HSHNRNPA gcgccaactaggtatgaaggacaactgctgacagtg acaatgatttggtgtaccaagtggataaggctcagt gcaggggcctaggctaattgcggcttgagagcgctg ROA1_DROME VMKDPRTKRSRGFGFITYSHSSMIDE VM+DP TKRSRGFGF+TY+ +D VMRDPNTKRSRGFGFVTYATVEEVDA HSHNRNPA GTAAGAT Intron 1 CAGgaagcaaactagtgtgatgagggggg <0-----[1314 : 1608]-0>ttgacacagcggtgttcacctaatac agataccgctgctgtcatctggggta ROA1_DROME AQKSRPHKIDGRVVEPKRAVPRQ DID A +RPHK+DGRVVEPKRAV R D AMNARPHKVDGRVVEPKRAVSRE DSQ HSHNRNPA gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc ctacgcaataggttacagctcga<0-----[1756 : 1903]-0>aca tgtagacggtaatgaagatccaa tta ROA1_DROME SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDINIVIDKETGKK P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK HSHNRNPA acggctagaaatgggaaggaggcccagttgctgaaggagaaagcgagaa gcgcatctaatttggtaaacaaaatgaataaagatattattcaggggaa aatccatgagatttctaactaatcaatttagtaatagtacgtcactcga

20 Alignment 1 Score 35.31 (Bits) Ex 2
SEED CAPNN-PCSNGGTCVNTPGGSSDNFGGYTCECPPGDYYLSYTGKRC CA++ C++ +CVN C+C PG Y L+ + K C CAEGGHGCQH--QCVNAWA MFHCTCNPG-YKLAADNKSC EM:HS453C tggggcgtcc ctgagtg atctatacg tacgggaaat gcaggaggaa agtacgc ttagcgacg aatccaaagg ttggattcgc atctcgc gccccccac CGAAATCGCT Alignment 2 Score (Bits) CA+++ C + CVN+PG Y+C+C++G +L+ + + C CAEGTHGCEH--HCVNSPG SYFCHCQVG-FVLQQDQRSC EM:HS453C tgggacgtgc ctgatcg ttttctcgg tgcccgcaat gcagcaggaa agtaccg catgagatg tttaaaaggg ttagctatgc ccctcac ctctccatc tacggcggcc Ex 2

21 tggcatggggcgcaggttctctatacaccccccgcccccggctgccaggctctgcggcctcaccttggaactacagggcaagagcttcttccagggggtgaggttttcggtgcagaccacctcccgcggcagcacagcatagcgcagaaagtagtggtcagtgtctgagggagacagaggtctgtctggggtgggccttgggctctgacccctcgggatccacattccagagatgggaatgaccctcctgctccccacaccacctctagcaccacagtctggacagtcccaactgggagtaggactcccttctctccttgggaaaaggcatgcagagatggcacagtattgggggcctgcacacacaggggacttaggatctagcccaggctgaggaagcaggaaactgagggaaaaggaggcaaaggtttgggcaggaggtaagaggaagaaggaaagggctgtaggggttatctcaccattggccagacccaggggtttgaaggaggcagtgggagtgactgtgttggtggagtcgatgaagttgagagaggcgcagaagatccctgagaggacattactgagctccttccaagatttatccacactggatagagacacaaatccactcactgtcctggggctacctctgctccctctttcaaagtccacagctggctgctaaacctatgataggaggaggctgtattcttaactattagacgggccagttgatggagctggaacattgctgcccccagccagcccacttgctgggtctcatcctactcagccccttcttcctcactctcctctggacatctctgcatccccatgggtctctgctcaggtgattcttccttccttgcaagcctttgctaacttctttctgcctaccttcatgatccggctccagtgcttacctcccctccacgaagcctttcctgccctccttaagcacagtctcctctgtgcagtcacggttctgaccatccaagcatcttactaggtccctcctgggagatggctaggtggcagcagcatcgtgtcctgaccaccttttctccctaactaggctgtaagcaacttgaggacaaggaccagtctgggtcatctatgtacttcccctgacaccatggaaagcgcctcatgtatcagagctgaaatgagctcactgatcttccttgaatgtgctgggctgggcaaaacaatgcatactaccctgtgtatactctgggaataaaggtaagtcctgattctactatcatggtgagaagtcttatatccaaaaaagctcactgaacatgggaaaaacaactgttctaggatttcataaaaacatcaaattaaattaatgttcttttcttggagaaatatcaaaagagatttgctctcagtaatagagaaagcataaaacttaataagcactagaaagaattctaagcatttgctccacatttcaggcaattacgggctgagggaagacagtgacagcagagtagacaggaaagggtaggggagccagagttgaggcaagagagaaagtcttggcaagctggggagttactgcttattccttattccttagtgttgtccaggagcttttgataattctatgttcagagcttttcaactgctccaatccttaagcctcaaataaaaatggcaaacttgaagccggaaagctctactcaaaccataaacatgcttcatttggtatgcacaacattgacccgcacagcactcaaaaaatttttaaattacttgctgatatttgaatttgccaattttcacattaaattccagatttctggtatctcttgaaaaatgaggccaggtgtggtggctcttgcctgtaatcccaacactttgggaggctgaggcaggaggatCGCTtgaacccaggagttcgagaccagcctgggcaatatagtgagaccttgtttctacaaaaaatttttagaaacatttgactctgaccacattaggcctctattcccacatggcaacaatccatagaagctgagtggcagagctgtcctcg