Hi, I would like to know if there is any function that can extend the function matchPattern (Biostrings package) to be able to also find indels of any given size. Best regards João Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: Joao.Fadista@agrsci.dk <mailto:joao.fadista@agrsci.dk> Web: www.agrsci.org <http: www.agrsci.org=""/> ________________________________ DJF now offers new degree programmes <http: www.agrsci.org="" content="" view="" full="" 34133=""> . Subscribe to newsletter <http: www.agrsci.dk="" user="" register?lan="dan-" dk=""> . 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]]

Jo?o, The pairwiseAlignment function in the Biostrings package can find indels in alignments. The Alignments vignette in the Biostrings package gives a comprehensive overview of using this function. See if this meets your needs. Patrick Jo?o Fadista wrote: > Hi, > > I would like to know if there is any function that can extend the function matchPattern (Biostrings package) to be able to also find indels of any given size. > > > > Best regards > > Jo?o Fadista > Ph.d. student > > > > UNIVERSITY OF AARHUS > Faculty of Agricultural Sciences > Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Phone: +45 8999 1900 > Direct: +45 8999 1900 > E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> > Web: www.agrsci.org <http: www.agrsci.org=""/> > ________________________________ > > DJF now offers new degree programmes <http: www.agrsci.org="" content="" view="" full="" 34133=""> . > > Subscribe to newsletter <http: www.agrsci.dk="" user="" register?lan="dan-" dk=""> . > > > > > [[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