Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions
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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2019-07-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2018-0090 |
| _version_ | 1818736914915655680 |
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| author | Li Yaoyong Aguilar-Martinez Elisa Sharrocks Andrew D. |
| author_facet | Li Yaoyong Aguilar-Martinez Elisa Sharrocks Andrew D. |
| author_sort | Li Yaoyong |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-18T00:44:44Z |
| format | Article |
| id | doaj.art-e0eb36ba019f4801b72dcffe5ffb927c |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-18T00:44:44Z |
| publishDate | 2019-07-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-e0eb36ba019f4801b72dcffe5ffb927c2022-12-21T21:26:48ZengDe GruyterJournal of Integrative Bioinformatics1613-45162019-07-01163D6263410.1515/jib-2018-0090jib-2018-0090Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein RegionsLi Yaoyong0Aguilar-Martinez Elisa1Sharrocks Andrew D.2School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UKSchool of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UKSchool of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UKThe 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.https://doi.org/10.1515/jib-2018-0090genomicsproteomicsmapping between genome and proteomedna sequencesprotein sequences |
| spellingShingle | Li Yaoyong Aguilar-Martinez Elisa Sharrocks Andrew D. Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions Journal of Integrative Bioinformatics genomics proteomics mapping between genome and proteome dna sequences protein sequences |
| title | Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions |
| title_full | Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions |
| title_fullStr | Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions |
| title_full_unstemmed | Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions |
| title_short | Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions |
| title_sort | geno2proteo a tool for batch retrieval of dna and protein sequences from any genomic or protein regions |
| topic | genomics proteomics mapping between genome and proteome dna sequences protein sequences |
| url | https://doi.org/10.1515/jib-2018-0090 |
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