1,721,042 research outputs found
Internet resources for the functional analysis of 5 ' and 3 ' untranslated regions of eukaryotic mRNAs
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Reorganization and merging of the EMBL and GenBank keyword indexes in a tree structure for more efficient retrieval of nucleic acid sequences.
No full textEMBL and GenBank keyword indexes have no hierarchical structure. In this paper we present a method for merging and reorganizing them in a tree structure whose primary roots are the keywords 'protein', 'DNA', 'RNA', and 'unclassified'. Synonymous keywords have been grouped together and erroneous keywords have been corrected. This taxonomic organization of keywords results in a more extensive and efficient retrieval which is further aided by "synonyms declaration". The tree has been produced using the computer programs GENPOINT and CREANET
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
No full textThe untranslated regions of eukaryotic mRNAs: structure, function, evolution and bioinformatic tools for their analysis
No full textThe crucial role of the non-coding portion of genomes is now widely acknowledged. In particular, mRNA untranslated regions are involved in many post-transcriptional regulatory pathways that control mRNA localisation, stability and translation efficiency. A review is given of the most recent research works on the functional characterisation of eukaryotic mRNA untranslated regions. In order to make possible a systematic and detailed sequence analysis of mRNA untranslated regions (UTRs), a non-redundant database of metazoan mRNA untranslated sequences annotated for the occurrence of specific functional elements, UTRdb, was devised. These elements, whose consensus structure has been devised on the basis of experimental assays and of comparative analyses, have been collected in the UTRsite database. A suitable pattern-matching software has been devised to search UTRsite patterns in user-submitted sequences, also assessing their statistical significance. Structural, compositional and evolutionary features of untranslated sequences of metazoan mRNAs have been investigated showing peculiar intra- and interspecific patterns
Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis
No full textFASTPAT - A FAST AND EFFICIENT ALGORITHM FOR STRING SEARCHING IN DNA-SEQUENCES
No full textA new string searching algorithm is Presented aimed at searching for the occurrence of character patterns in longer character texts. The algorithm, specifically designed for nucleic acid sequence data, is essentially derived from the Boyer-Moore method (Comm. ACM, 20, 762-772, 1977). Both pattern and text data are compressed so that the natural 4-letter alphabet of nucleic acid sequences is considerably enlarged. The string search starts from the last character of the pattern and proceeds in large jumps through the text to be searched. The data compression and searching algorithm allows one to avoid searching for patterns not present in the text as well as to inspect, for each pattern, all text characters until the exact match with the text is found. These considerations are supported by empirical evidence and comparisons with other methods
Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
No full textThe AMmtDB database (http://bio-www.ba.cnr,it:8000/srs6/) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for:proteins and tRNAs, The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using:GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually
Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis
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