Asaf Salamov

The Trichoplax genome and the nature of placozoans

As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the ∼98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a ‘eumetazoan’ clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.

The DNA sequence and biology of human chromosome 19

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

Assessing protein coding region integrity in cDNA sequencing projects.

MOTIVATION In cDNA sequencing projects, it is vital to know whether the protein coding region of a sequence is complete, or whether errors have occurred during library construction. Here we present a linear discriminant approach that predicts this completeness by estimating the probability of each ATG being the initiation codon. RESULTS Because of the current shortage of full-length cDNA data on which to base this work, tests were performed on a non-redundant set of 660 initiation codon-containing DNA sequences that had been conceptually spliced into mRNA/cDNA. We also used an edited set of the same sequences that only contained the region following the initiation codon as a negative control. Using the criterion that only a single prediction is allowed for each sequence, a cut-off was selected at which discrimination of both positive and negative sets was equal. At this cut-off, 67% of each set could be correctly distinguished, with the correct ATG codon also being identified in the positive set. Reliability could be increased further by raising the cut-off or including homologues, the relative merits of which are discussed. AVAILABILITY The prediction program, called ATGpr, and other data are available at http://www.hri.co.jp/atgpr CONTACT swintech@hri.co.jp

Predicting α-helix and β-strand segments of globular proteins

All current methods of protein secondary structure prediction are based on evaluation of a single residue state. Although the accuracy of the best of them is approximately 60-70%, for reliable prediction of tertiary structure it is more useful to predict an approximate location of alpha-helix and beta-strand segments, especially prolonged ones. We have developed a simple method for protein secondary structure prediction which is oriented on the location of secondary structure segments. The method uses linear discriminant analysis to assign segments of a given amino acid sequence a particular type of secondary structure, by taking into account the amino acid composition of internal parts of segments as well as their terminal and adjacent regions. Four linear discriminant functions were constructed for recognition of short and long alpha-helix and beta-strand segments respectively. These functions combine three characteristics: hydrophobic moment, segment singlet, and pair preferences to an alpha-helix or beta-strand. The last two characteristics are calculated by summing the preference parameters of single residues and pairs of residues located in a segment and its adjacent regions. The final program SSP predicts all possible potential alpha-helices and beta-strands and resolves some possible overlap between them. Overall three-state (alpha, beta, c) prediction gives approximately 65.1% correctly predicted residues on 126 non-homologous proteins using the jackknife test procedure. Analysis of the prediction results shows a high prediction accuracy of long secondary structure segments (approximately 89% of alpha-helices of length > 8 and approximately 71% of beta-strands of length > 6 are correctly located with probability of correct prediction 0.82 and 0.78 respectively.(ABSTRACT TRUNCATED AT 250 WORDS)