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Pràctiques Bioinformàtica - Perl

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by

Carla Giner

on 14 November 2013

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Transcript of Pràctiques Bioinformàtica - Perl

Input GenBank $db_obj get_Seq_by_acc($acc) acc1 acc2 acc4 ... acc3 $seq_obj subseq(S,E) $subseq_obj %genbank_acc foreach $acc
(keys %genbank_acc) S-E S-E S-E S-E ... push(@subseqs, $subseq_obj) @subseqs seq1 seq2 seq3 seq4 seq5 seq6 ... $aln_obj spikeCDS_aln.clustal spikeCDS_aln.fasta spikeCDS_aln.mega $alnio_obj_clustal write_aln($aln_obj) Input Bio::DB::GenBank GenBank $db_obj get_Seq_by_acc($acc) acc1 acc2 acc4 ... acc3 $seq_obj @genbank_acc foreach $acc
(@genbank_acc) push(@seqs, $subseq_obj) @seqs seq1 seq2 seq3 seq4 seq5 seq6 ... $aln_obj spike_aln.clustal spike_aln.fasta spike_aln.mega $alnio_obj_clustal write_aln($aln_obj) Programa 3:
alineament Spike CDS
de diferents individus Programa 2:
alineament proteïna Spike
de diferents hostes Programa 1:
genoma del virus SARS-CoV Input GenBank $db_obj get_Seq_by_acc($genbank_acc) $seq_obj Bio::DB::GenBank $genbank_acc desc division molecule species->node_name length Imprimir informació
per pantalla Bio::SeqIO Bio::Tools::Run::Alignment::Clustalw Bio::AlignIO Bio::DB::GenBank Bio::Seq Bio::Tools::Run::Alignment::Clustalw SARS-CoV.fasta SARS-CoV.gb $seqio_obj_fasta $seqio_obj_genbank write_seq($seq_obj) Bio::AlignIO $alnio_obj_fasta $alnio_obj_mega $alnio_obj_fasta $alnio_obj_mega $factory $factory Desar la seqüència Descarregar seqüències Alinear Desar l'alineament Alinear Desar l'alineament Descarregar i processar seqüències Descarregar
seqüència Pràctiques de Bioinformàtica
Programació en Perl align(\@seqs) align(\@subseqs)
Full transcript