Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

SUMMARY: Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs. AVAILABILITY: Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally.     

A standardized format for handling data on plasmids,viruses and transposons: The PVT database format

The PVT format described here has been designed to store and retrieve genetic data on plasmids, viruses or transposons with special focus on their applications. Both naturally-occurring and engineered elements can be included in it. A variety of data can be accommodated in fields that are grouped in blocks: name and type of element, database administration, element administration, history, propagation, selection and host, biological properties, cloned insert and applications. The number of fields, now 157, can be expanded as required. Most properties can be described in simple logical fields. The format is organized to permit rapid searches and to facilitate communication between database and user; connection with culture and/or DNA collections is also envisaged and adequate fields for these tasks have been provided. The format allows cross-reference with that originated by the Microbial Information Network Europe (MINE) for computer storage and handling of bacterial or fungal strain data.     

The histone variant CENP-A and centromere specification

The centromere is the chromosomal locus that guides faithful inheritance. Centromeres are specified epigenetically, and the histone H3 variant CENP-A has emerged as the best candidate to carry the epigenetic centromere mark. Recent advances demonstrate the physical basis for this epigenetic mark whereby CENP-A confers conformational rigidity to the nucleosome it forms with other core histones. This nucleosome is recognized by a multisubunit complex of constitutive centromere proteins, termed the CENP-A(NAC). Evidence from two CENP-A relatives in diverse eukaryotes suggests that the histone complexes they form adopt highly unconventional arrangements on DNA. Centromere identity, itself, is propagated during mitotic exit and early G1, and it relies upon a cis-acting targeting domain within CENP-A and a proposed centromere 'priming' reaction.     

The significance of call duration in howler monkeys

The “loud” calls of forest primates consist of repeated sounds that elicit a response from other members of the species. Recent studies suggest that these calls are often displays by the males that permit them to assess the strength of their opponents. Previous research on red howler monkeys supported the hypothesis that howling functions in assessment of competing individuals, as an alternative to energetically expensive chases and fights. As the second step in the attempt to understand the evolution of howling in genus Alouatta,one aspect—call duration — was compared in two species,the mantled howler (Alouatta palliata)and the red howler (A. seniculus).In A. palliatathe median howl duration was 3.5 sec and the interhowl interval was 20.0 sec, while in A. seniculusthe median howl duration was 19.0 sec and the interhowl interval was 3.0 sec. During the dawn chorus, the total duration of calling in A. seniculusmay be 10 or more times greater than that in A. palliata.The latter species appears to be limited in the duration of howls it can produce, so it increases the amount of calling by reducing the interhowl interval. At least four factors may be important in the evolution of the observed differences in call structure: constraints of the acoustic environment, alternate forms of display used by A. palliata,the presence or absence of competing males within the troop, and the effect of female calls on male howling. The observations suggest that the use of the male loud call may reflect differences in the nature of male-male competition and female support more than it reflects the constraints of the acoustic environment.