Publications - Working papers
Please find below working papers of our group. Currently, we list 58 working papers.
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RNAcode Web – Convenient Identification of Evolutionary Conserved Protein Coding Regions
John Anders, Peter F Stadler
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Status: In preparation
Journal of Integrative Bioinformatics (JIB)
Abstract
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 coding sequence detector RNAcode with minimal use 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, and the construction of the multiple sequence alignment requires are input for RNAcode. The service make 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
Keywords
coding sequence detection, comparative genomics, small peptides