VIP DB--a viral protein domain usage and distribution database.

During the viral infection and replication processes, viral proteins are highly regulated and may interact with host proteins. However, the functions and interaction partners of many viral proteins have yet to be explored. Here, we compiled a VIral Protein domain DataBase (VIP DB) to associate viral proteins with putative functions and interaction partners.

DSAP: deep-sequencing small RNA analysis pipeline.

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.

Identification of microRNA in the protist Trichomonas vaginalis.

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. However, miRNA has never been identified experimentally in protist. Direct cloning of 438 expressed miRNA tags by microRNA serial analysis of gene expression from the parasitic protist Trichomonas vaginalis identified nine candidate miRNAs.

A proteome reference map of Trichomonas vaginalis.

Trichomoniasis caused by Trichomonas vaginalis is the most common sexual transmitted infection in the world. The 170-MB genome of this protozoan contains 60,000 genes, the largest number of genes ever identified in protozoan. High-throughput expression sequenced tag analysis showed that at least 4,000 genes were expressed in the trophozoite stage.