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J Integr Bioinform. 2019 Jul 13;16(3). pii: /j/jib.2019.16.issue-3/jib-2018-0090/jib-2018-0090.xml. doi: 10.1515/jib-2018-0090.

Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions.

Author information

1
School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

Abstract

The interconversion of sequences that constitute the genome and the proteome is becoming increasingly important due to the generation of large amounts of DNA sequence data. Following mapping of DNA segments to the genome, one fundamentally important task is to find the amino acid sequences which are coded within a list of genomic sections. Conversely, given a series of protein segments, an important task is to find the genomic loci which code for a list of protein regions. To perform these tasks on a region by region basis is extremely laborious when a large number of regions are being studied. We have therefore implemented an R package geno2proteo which performs the two mapping tasks and subsequent sequence retrieval in a batch fashion. In order to make the tool more accessible to users, we have created a web interface of the R package which allows the users to perform the mapping tasks by going to the web page http://sharrocksresources.manchester.ac.uk/tofigaps and using the web service.

KEYWORDS:

DNA sequences; Genomics; Mapping between genome and proteome; Protein sequences; Proteomics

PMID:
31301672
PMCID:
PMC6798850
DOI:
10.1515/jib-2018-0090
[Indexed for MEDLINE]
Free PMC Article

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