Mutation or deletion of ADAR genes results in striking phenotypes, including seizure episodes, extreme uncoordination, and neurodegeneration. Most RNA editing sites in these nervous system targets result in non-synonymous codon changes in functionally important, usually conserved, residues and RNA editing deficiencies in various model organisms bear out a crucial role for ADARs in nervous system function. Once in the nucleus, ADARs participate in the modification of specific adenosines in pre-mRNAs of proteins involved in electrical and chemical neurotransmission, including pre-synaptic release machineries, and voltage- and ligand-gated ion channels. ADAR family members are highly expressed in the metazoan nervous system, where these enzymes predominantly localize to the neuronal nucleus. All ADARs share a common domain architecture consisting of a variable number of amino-terminal dsRNA binding domains (dsRBDs) and a carboxy-terminal catalytic deaminase domain. A highly conserved group of enzymes, the adenosine deaminase acting on RNA (ADAR) family, mediates this reaction. lessAdenosine to inosine (A-to-I) RNA editing is a post-transcriptional process by which adenosines are selectively converted to inosines in double-stranded RNA (dsRNA) substrates. MacVector also comes with a module for contig assembly, called AssemblyLIGN. At the time of writing, the version of MacVector available was 6.5. It provides all of the most commonly used nucleic acid and protein analysis tools and also provides access via the Internet to the public Entrez databases at the National Center for Biotechnology Information (NCBI). It is an integrated comprehensive sequence analysis program that runs on the Macintosh.
MacVector™, from Oxford Molecular Group, Campbell CA, is one such computer package. It is evident by now that efficiently performing the above operations on thousands or millions of base pairs by hand is so difficult as to be impossible, and computer programs that do sequence analysis are becoming more and more ubiquitous in laboratories practicing molecular biology. Whether a researcher is working on a genome project, or is cloning and characterizing a gene of interest, the ability to manipulate, analyze, and annotate sequence data is becoming increasingly important. (1983) Rapid similarity searches of nucleic acid and protein databanks. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. (1985) Rapid and sensitive protein similarity searches. (1982) A high speed, high capacity homology matrix zooming through SV40 and polyoma. (1994) Issues in searching molecular sequence databases. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. (1974) Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. (1984) The codon preference plot graphic analysis of protein coding sequences and prediction of gene expression.
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