MPBLAST : improved BLAST performance with multiplexed queries

SUMMARY: We have developed a program, MPBLAST, that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed. Throughput was observed to increase in reciprocal proportion to the component sequence length. For sequencing read-sized queries of 500 bp, an order of magnitude speed-up was seen. AVAILABILITY: Free (see http://blast.wustl.edu) CONTACT: [ikorf, gish]@watson.wustl.edu     

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users.     

ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets

ViroBLAST is a stand-alone BLAST web interface for nucleotide and amino acid sequence similarity searches. It extends the utility of BLAST to query against multiple sequence databases and user sequence datasets, and provides a friendly output to easily parse and navigate BLAST results. ViroBLAST is readily useful for all research areas that require BLAST functions and is available online and as a downloadable archive for independent installation. Availability: http://indra.mullins.microbiol.washington.edu/blast/viroblast.php.     

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries

Expressed sequence tags (ESTs) are randomly sequenced cDNA clones. Currently, nearly 3 million human and 2 million mouse ESTs provide valuable resources that enable researchers to investigate the products of gene expression. The EST databases have proven to be useful tools for detecting homologous genes, for exon mapping, revealing differential splicing, etc. With the increasing availability of large amounts of poorly characterised eukaryotic (notably human) genomic sequence, ESTs have now become a vital tool for gene identification, sometimes yielding the only unambiguous evidence for the existence of a gene expression product. However, BLAST-based Web servers available to the general user have not kept pace with these developments and do not provide appropriate tools for querying EST databases with large highly spliced genes, often spanning 50 000-100 000 bases or more. Here we describe Gene2EST (http://woody.embl-heidelberg.de/gene2est/), a server that brings together a set of tools enabling efficient retrieval of ESTs matching large DNA queries and their subsequent analysis. RepeatMasker is used to mask dispersed repetitive sequences (such as Alu elements) in the query, BLAST2 for searching EST databases and Artemis for graphical display of the findings. Gene2EST combines these components into a Web resource targeted at the researcher who wishes to study one or a few genes to a high level of detail.     

Production of rats in synchronised batches.

Successful synchronisation of copulations and births for the 1st parity permit continued synchrony of parturitions in subsequent parities. Foetal implantation after post-partum copulation was delayed by multiples of the oestrous cycle; both season and number of sucking neonates influenced the time of implantation. Post-weaning matings gave a high conception rate with a parturition spread of 36 hours for 94% of the original group.     

BLAST+: architecture and applications

Background  

Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.     

Improved gapped alignment in BLAST

Homology search is a key tool for understanding the role, structure, and biochemical function of genomic sequences. The most popular technique for rapid homology search is BLAST, which has been in widespread use within universities, research centers, and commercial enterprises since the early 1990s. We propose a new step in the BLAST algorithm to reduce the computational cost of searching with negligible effect on accuracy. This new step - semigapped alignment - compromises between the efficiency of ungapped alignment and the accuracy of gapped alignment, allowing BLAST to accurately filter sequences with lower computational cost. In addition, we propose a heuristic - restricted insertion alignment - that avoids unlikely evolutionary paths with the aim of reducing gapped alignment cost with negligible effect on accuracy. Together, after including an optimization of the local alignment recursion, our two techniques more than double the speed of the gapped alignment stages in blast. We conclude that our techniques are an important improvement to the BLAST algorithm. Source code for the alignment algorithms is available for download at http://www.bsg.rmit.edu.au/iga/.     

Evolutionary genomics: yeasts accelerate beyond BLAST

Two new genome sequences confirm that a whole genome duplication occurred in an ancestor of Saccharomyces cerevisiae. This left a legacy of about 500 pairs of duplicated genes, many of which contribute to this yeast's ability to ferment glucose anaerobically; a few have been evolving so quickly they retain almost no sequence similarity to each other.     

Tracker: continuous HMMER and BLAST searching

SUMMARY: Tracker is a web-based email alert system for monitoring protein database searches using HMMER and Blast-P, nucleotide searches using Blast-N and literature searches of the PubMed database. Users submit searches via a web-based interface. Searches are saved and run against updated databases to alert users about new information. If there are new results from the saved searches, users will be notified by email and will then be able to access results and link to additional information on the NCBI website. Tracker supports Boolean AND/OR operations on HMMER and BLASTP result sets to allow users to broaden or narrow protein searches. AVAILABILITY: The server is located at http://jay.bioinformatics.ku.edu/tracker/index.html. A distribution package including detailed installation procedure is freely available from http://jay.bioinformatics.ku.edu/download/tracker/.     

Variations of sperm release in three batches of zebrafish

By collecting and counting the number of sperm released during separate matings in three batches of zebrafish Danio rerio , aged 3–4, 4–5 and 5–6 months, males were observed to release sperm before the female started laying their eggs. After the female left the nest, the number and motility of sperm and life span of sperm of younger fish were higher than those of older fish in water samples collected under the nest and at the surface of the tank. Sperm were released in the form of sperm trails laid on the nest surface, subsequently active spermatozoa left the trails and moved in the water for several minutes. Sperm trails consisted of bands of viscous material in which the sperm were embedded. In most cases eggs were not laid directly over the sperm trail, suggesting that sperm may contact the eggs after the latter are released into the water. In all the three tested groups there was no significant difference ( P  > 0·05) between the number of sperm collected on some portions of the acetate sheets which lined the nest ceiling. This result demonstrated that the greater activity of younger fish accelerated the sperm dispersal in water. Male sperm duct glands, seminal vesicles, known to secrete mucosubstances are probably involved in the production of sperm trails. The possible influence of insemination on the mating style of zebrafish is discussed.     

Outlier detection in BLAST hits

Background

An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of known sequences. Many approaches use the best BLAST hit(s) to assign the taxonomic label. However, it is known that the best BLAST hit may not always correspond to the best taxonomic match. An alternative approach involves phylogenetic methods, which take into account alignments and a model of evolution in order to more accurately define the taxonomic origin of sequences. Similarity-search based methods typically run faster than phylogenetic methods and work well when the organisms in the sample are well represented in the database. In contrast, phylogenetic methods have the capability to identify new organisms in a sample but are computationally quite expensive.

Results

We propose a two-step approach for metagenomic taxon identification; i.e., use a rapid method that accurately classifies sequences using a reference database (this is a filtering step) and then use a more complex phylogenetic method for the sequences that were unclassified in the previous step. In this work, we explore whether and when using top BLAST hit(s) yields a correct taxonomic label. We develop a method to detect outliers among BLAST hits in order to separate the phylogenetically most closely related matches from matches to sequences from more distantly related organisms. We used modified BILD (Bayesian Integral Log-Odds) scores, a multiple-alignment scoring function, to define the outliers within a subset of top BLAST hits and assign taxonomic labels. We compared the accuracy of our method to the RDP classifier and show that our method yields fewer misclassifications while properly classifying organisms that are not present in the database. Finally, we evaluated the use of our method as a pre-processing step before more expensive phylogenetic analyses (in our case TIPP) in the context of real 16S rRNA datasets.

Conclusion

Our experiments make a good case for using a two-step approach for accurate taxonomic assignment. We show that our method can be used as a filtering step before using phylogenetic methods and provides a way to interpret BLAST results using more information than provided by E-values and bit-scores alone.

     

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

SUMMARY: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide query sequence with any genomic region of interest, BLAST2GENE processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment. The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region. AVAILABILITY: The program is available upon request from the authors. A web server of BLAST2GENE is maintained at http://www.bork.embl.de/blast2gene     

Serial BLAST searching

MOTIVATION: The translating BLAST algorithms are powerful tools for finding protein-coding genes because they identify amino acid similarities in nucleotide sequences. Unfortunately, these kinds of searches are computationally intensive and often represent bottlenecks in sequence analysis pipelines. Tuning parameters for speed can make the searches much faster, but one risks losing low-scoring alignments. However, high scoring alignments are relatively resistant to such changes in parameters, and this fact makes it possible to use a serial strategy where a fast, insensitive search is used to pre-screen a database for similar sequences, and a slow, sensitive search is used to produce the sequence alignments. RESULTS: Serial BLAST searches improve both the speed and sensitivity.     

Mg++-sensitivity of neuromuscular transmission in two crustaceans: Correlation with blood Mg++ levels

Neuromuscular transmission was measured in muscles of spider crabs (Hyasareneus) and lobsters (Homarus americanus). Solutions containing 40 and 10 mM/1 Mg⁺⁺, which were approximately the same as those measured in the blood of Hyas and Homarus, respectively, were used to soak the preparations prior to testing. In Homarus, neuromuscular transmission was severely depressed by 40 mM Mg⁺⁺. In spider crabs, neuromuscular transmission was not severely depressed. Although the amount of transmitter released by nerve impulses was reduced, total membrane depolarization during trains of impulses was not reduced because a compensating increase in muscle fiber membrane resistance occurred in Hyas preparations exposed to 40 mM Mg⁺⁺. Hyas, but not Homarus, is physiologically adapted to function at relatively high blood Mg⁺⁺ concentrations.