Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of the computing power in the world is devoted to finding similarities between biological sequences. The introduction of optimal spaced seeds in [Ma et al., Bioinformatics 18 (2002) 440–445] has increased both the sensitivity and the speed of homology search and it h...

Profile Hidden Markov Models (PHMMs) are recognized as powerful computational vehicles for homology search of protein sequences. Extant PHMM training approaches either use completely unaligned or aligned sequences. The PHMMs resulting from these two training approaches present contrasting tradeoffs w.r.t. alignment information and the accuracy of the search outcome. This paper describes a PHMM ...

conclusions based on the location of detected rccs in the structure of hbv proteins, it was found that these rccs may have a critical role in correct folding of hbv proteins and can be considered as drug targets. the results of this study provide new and deep perspectives about structure of hbv proteins for further researches and designing new drugs for treatment of hbv. results the pfam search...

The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representa...

As a result of decoding of extensive genome sequences, a large number of proteins whose function cannot be predicted by the homology search of amino acid sequences is progressively accumulated and thus remains of no use in science and industry. A method to predict the protein function that does not depend on the sequence homology search is in urgent need. We previously developed a Batch-Learnin...

Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the...

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail ([email protected]) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows ...

Rad51 and Rad54 proteins are important for the repair of double-stranded DNA (dsDNA) breaks by homologous recombination in eukaryotes. Rad51 assembles on single-stranded DNA (ssDNA) to form a helical nucleoprotein filament that performs homologous pairing with dsDNA; Rad54 stimulates this pairing substantially. Here, we demonstrate that Rad54 acts in concert with the mature Rad51-ssDNA filament...

Circulating autoantibodies against tumor-associated antigens (TAAs) and their pattern of glycosylation can be used as diagnostic indicators of cancer. Using random peptide library screening, we identified patient-specific sets of peptides recognized by colon cancer patients' serum IgG and IgM antibodies. We demonstrate a strategy for analyzing BLAST search results for identifying tumor-associat...

Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synapton...