Hi, I would like to know if there is any bioconductor (or other) tool that is able to retrieve a batch of sequences from a fasta file, given the desired genomic coordinates. Desired genomic coordinates: chr1 1 5 chr2 8 13 Example of a fasta input file: >pig_chr1 acacactagagata >pig_chr2 gagagagcgcgcatgtgt Example of a fasta output file: >pig_chr1_start1_end5 acaca >pig_chr2_start8_end13 cgcgca Med venlig hilsen / Regards João Fadista Ph.d. studerende / Ph.d. student AARHUS UNIVERSITET / UNIVERSITY OF AARHUS Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Tel: +45 8999 1900 Direct: +45 8999 1342 Mobile: +45 E-mail: Joao.Fadista@agrsci.dk <mailto:joao.fadista@agrsci.dk> Web: www.agrsci.dk <http: www.agrsci.dk=""/> ________________________________ DJF udbyder nye uddannelser <http: www.agrsci.dk="" ny_navigation="" uddannelse=""/> / DJF now offers new degree programmes <http: www.agrsci.org="" content="" view="" full="" 34133=""> . Tilmeld dig DJF's nyhedsbrev / Subscribe Faculty of Agricultural Sciences Newsletter <http: www.agrsci.dk="" user="" register?lan="dan-DK"> . Denne email kan indeholde fortrolig information. Enhver brug eller offentliggørelse af denne email uden skriftlig tilladelse fra DJF er ikke tilladt. Hvis De ikke er den tiltænkte adressat, bedes De venligst straks underrette DJF samt slette emailen. This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]]

Hi Jo?o, Jo?o Fadista wrote: > Hi, > > I would like to know if there is any bioconductor (or other) tool that is able to retrieve a batch of sequences from a fasta file, given the desired genomic coordinates. > > Desired genomic coordinates: > chr1 1 5 > chr2 8 13 > > Example of a fasta input file: >> pig_chr1 > acacactagagata >> pig_chr2 > gagagagcgcgcatgtgt > > Example of a fasta output file: >> pig_chr1_start1_end5 > acaca >> pig_chr2_start8_end13 > cgcgca > library(Biostrings) > tmp <- read.DNAStringSet("pig.fa","fasta") Read 4 items > tmp A DNAStringSet instance of length 2 width seq names [1] 14 ACACACTAGAGATA pig_chr1 [2] 18 GAGAGAGCGCGCATGTGT pig_chr2 > tmp[[1]][1:5] 5-letter "DNAString" instance seq: ACACA > tmp[[2]][8:13] 6-letter "DNAString" instance seq: CGCGCA > as.character(tmp[[1]][1:5]) [1] "ACACA" Best, Jim > > > > > > Med venlig hilsen / Regards > > Jo?o Fadista > Ph.d. studerende / Ph.d. student > > > > AARHUS UNIVERSITET / UNIVERSITY OF AARHUS > Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences > Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Tel: +45 8999 1900 > Direct: +45 8999 1342 > Mobile: +45 > E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> > Web: www.agrsci.dk <http: www.agrsci.dk=""/> > ________________________________ > > DJF udbyder nye uddannelser <http: www.agrsci.dk="" ny_navigation="" uddannelse=""/> / DJF now offers new degree programmes <http: www.agrsci.org="" content="" view="" full="" 34133=""> . > > Tilmeld dig DJF's nyhedsbrev / Subscribe Faculty of Agricultural Sciences Newsletter <http: www.agrsci.dk="" user="" register?lan="dan-DK"> . > > Denne email kan indeholde fortrolig information. Enhver brug eller offentligg?relse af denne email uden skriftlig tilladelse fra DJF er ikke tilladt. Hvis De ikke er den tilt?nkte adressat, bedes De venligst straks underrette DJF samt slette emailen. > > > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662