Selected Protein Sequences Research Articles

Frame: detection of genomic sequencing errors.

The underlying error rate for genomic sequencing sometimes results in the introduction of artificial frameshifts and in-frame stop codons into putative protein encoding genes. Severe errors are then introduced into the inferred transcripts through mis-translation or premature termination. We describe a system for screening segments of DNA for frameshift and in-frame stop errors in coding regions. The method is based on homology matching using blastx to compare all six reading frames of the query nucleotide sequence against selected protein sequence databases. Fragments of protein matching neighbouring regions of the query DNA are united and extended laterally to define candidate open reading frames, within which, frameshifts and stops are identified. Suitable targets include prokaryotic or other intron-free genomic sequence and complementary DNAs. As an example of its use, we report here two frameshifted ORFs that deviate from the original TIGR sequence annotations for the recently released Helicobacter pylori genome. The tool is accessible via the URL http://www.sander.ebi.ac.uk/frame/. brown@ebi.ac.uk.

Antipeptide antibodies against the 5-HT 1A receptor

The availability of the primary amino acid sequence for a large numbers of molecules provides a fruitful opportunity for their cellular localization by utilizing the procedure of antipeptide antibody formation. This procedure permits a synthetic peptide sequence to be attached to a carrier molecule for the purpose of inoculating an animal to raise specific antibodies against the selected protein sequence. In this report we describe a number of steps that can be taken to increase the likelihood that the selected peptide sequence will be specific and antigenic. In addition, we describe how the peptides are synthesized, purified and coupled to keyhold limpet hemocyanin. The preparation of the antibody and its characterization are also presented in this method report. The immunocytochemical staining at both the light and ultrastructural level with serotonin (5-HT 1A) receptor antipeptide antibodies is discussed. The advantages and disadvantages of this procedure are summarized.