OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures

The large number of experimentally determined protein 3D structures is a rich resource for studying protein function and evolution, and protein structure comparison (PSC) is a key method for such studies. When comparing two protein structures, almost all currently available PSC servers report a single and sequential (i.e. topological) alignment, whereas the existence of good alternative alignments, including those involving permutations (i.e. non-sequential or non-topological alignments), is well known. We have recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10(−5)), including structural permutations at all levels of complexity. OPAAS, the server of this PSC method freely accessible at our website (), provides an easy-to-read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected. Because these alternative alignments can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins, OPAAS can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing PSC servers

Transcriptome profiling of the fifth-stage larvae of Angiostrongylus cantonensis by next-generation sequencing

Angiostrongylus cantonensis is an important zoonotic nematode. It is the causative agent of eosinophilic meningitis and eosinophilic meningoencephalitis in humans. However, information of this parasite at the genomic level is very limited. In the present study, the transcriptomic profiles of the fifth-stage larvae (L5) of A. cantonensis were investigated by next-generation sequencing (NGS). In the NGS database established from the larvae isolated from the brain of Sprague–Dawley rats, 31,487 unique genes with a mean length of 617 nucleotides were assembled. These genes were found to have a 46.08 % significant similarity to Caenorhabditis elegans by BLASTx. They were then compared with the expressed sequence tags of 18 other nematodes, and significant matches of 36.09–59.12 % were found. Among these genes, 3,338 were found to participate in 124 Kyoto Encyclopedia of Genes and Genomes pathways. These pathways included 1,514 metabolisms, 846 genetic information processing, 358 environmental information processing, 264 cellular processes, and 91 organismal systems. Analysis of 30,816 sequences with the gene ontology database indicated that their annotations included 5,656 biological processes (3,364 cellular processes, 3,061 developmental processes, and 3,191 multicellular organismal processes), 7,218 molecular functions (4,597 binding and 3,084 catalytic activities), and 4,719 cellular components (4,459 cell parts and 4,466 cells). Moreover, stress-related genes (112 heat stress and 33 oxidation stress) and genes for proteases (159) were not uncommon. This study is the first NGS-based study to set up a transcriptomic database of A. cantonensis L5. The results provide new insights into the survival, development, and host–parasite interactions of this blood-feeding nematode. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00436-013-3495-z) contains supplementary material, which is available to authorized users

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing

Number of misassemblies for different assembly strategies. Number of misassemblies for the de novo assembly results for E. coli DH1 and S. Parasanguinis FW213 are shown together with their standard errors of the mean. Group A [PE] and Group A [SE] represent all reads assembled as paired-end reads and single end reads, respectively. Group A [PE + SE] represents all the non-overlapped paired-end reads assembled together with merged reads. Group M [PE] and Group M [SE] represent Group M reads assembled as paired-end reads and single end reads, respectively. The numbers of misassemblies fluctuate a lot when depths of read number are low and gradually decreases until they reach a steady number. The paired-end reads (Group A [PE] and Group M [PE]) in S. Parasanguinis FW213 gave the lowest number of misassemblies when depths of read number are high. (TIFF 669 kb

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.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log2-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw

Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis

Background/Purpose(s)Trichomoniasis caused by Trichomonas vaginalis is the most common non-viral sexually transmitted infection. Morphological transformation from the trophozoite stage to the amoeboid or pseudocyst stage is crucial for T. vaginalis infection and survival. Protein phosphorylation is a key post-translational modification involved in the regulation of several biological processes in various prokaryotes and eukaryotes. More than 880 protein kinases have been identified in the T. vaginalis genome. However, little is known about the phosphorylation of specific proteins and the distribution of phosphorylated proteins in different stages of the morphological transformation of T. vaginalis.MethodsTo obtain a more comprehensive understanding of the T. vaginalis phosphoproteome, we analyzed phosphorylated proteins in the three morphological stages using titanium dioxide combined with LC-MS/MS.ResultsA total of 93 phosphopeptides originating from 82 unique proteins were identified. Among these proteins, 21 were detected in all stages, 29 were identified in two different stages, and 32 were stage specific.ConclusionIdentification of stage-specific phosphorylated proteins indicates that phosphorylation of these proteins may play a key role in the morphological transformation of T. vaginalis