RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions
The differentiation of regions with coding potential from non-coding regions remains a key task in computational biology. Methods such as RNAcode that exploit patterns of sequence conservation for this task have a substantial advantage in classification accuracy in particular for short coding sequen...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2023-08-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2022-0046 |
| _version_ | 1797362069992898560 |
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| author | Anders John Stadler Peter F. |
| author_facet | Anders John Stadler Peter F. |
| author_sort | Anders John |
| collection | DOAJ |
| description | The differentiation of regions with coding potential from non-coding regions remains a key task in computational biology. Methods such as RNAcode that exploit patterns of sequence conservation for this task have a substantial advantage in classification accuracy in particular for short coding sequences, compared to methods that rely on a single input sequence. However, they require sequence alignments as input. Frequently, suitable multiple sequence alignments are not readily available and are tedious, and sometimes difficult to construct. We therefore introduce here a new web service that provides access to the well-known coding sequence detector RNAcode with minimal user overhead. It requires as input only a single target nucleotide sequence. The service automates the collection, selection, and preparation of homologous sequences from the NCBI database, as well as the construction of the multiple sequence alignment that are needed as input for RNAcode. The service automatizes the entire pre- and postprocessing and thus makes the investigation of specific genomic regions for previously unannotated coding regions, such as small peptides or additional introns, a simple task that is easily accessible to non-expert users. RNAcode_Web is accessible online at rnacode.bioinf.uni-leipzig.de. |
| first_indexed | 2024-03-08T16:03:16Z |
| format | Article |
| id | doaj.art-279f4419a2d54803950d3bdd13de88a7 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-03-08T16:03:16Z |
| publishDate | 2023-08-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-279f4419a2d54803950d3bdd13de88a72024-01-08T09:53:35ZengDe GruyterJournal of Integrative Bioinformatics1613-45162023-08-012032819210.1515/jib-2022-0046RNAcode_Web – Convenient identification of evolutionary conserved protein coding regionsAnders John0Stadler Peter F.1Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, D-04107Leipzig, GermanyBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, D-04107Leipzig, GermanyThe differentiation of regions with coding potential from non-coding regions remains a key task in computational biology. Methods such as RNAcode that exploit patterns of sequence conservation for this task have a substantial advantage in classification accuracy in particular for short coding sequences, compared to methods that rely on a single input sequence. However, they require sequence alignments as input. Frequently, suitable multiple sequence alignments are not readily available and are tedious, and sometimes difficult to construct. We therefore introduce here a new web service that provides access to the well-known coding sequence detector RNAcode with minimal user overhead. It requires as input only a single target nucleotide sequence. The service automates the collection, selection, and preparation of homologous sequences from the NCBI database, as well as the construction of the multiple sequence alignment that are needed as input for RNAcode. The service automatizes the entire pre- and postprocessing and thus makes the investigation of specific genomic regions for previously unannotated coding regions, such as small peptides or additional introns, a simple task that is easily accessible to non-expert users. RNAcode_Web is accessible online at rnacode.bioinf.uni-leipzig.de.https://doi.org/10.1515/jib-2022-0046coding sequence detectioncomparative genomicssmall peptides |
| spellingShingle | Anders John Stadler Peter F. RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions Journal of Integrative Bioinformatics coding sequence detection comparative genomics small peptides |
| title | RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions |
| title_full | RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions |
| title_fullStr | RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions |
| title_full_unstemmed | RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions |
| title_short | RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions |
| title_sort | rnacode web convenient identification of evolutionary conserved protein coding regions |
| topic | coding sequence detection comparative genomics small peptides |
| url | https://doi.org/10.1515/jib-2022-0046 |
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