BlaSTorage: a fast package to parse, manage and store BLAST results

Background: Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them. Findings: We implemented BlaSTorage, a Python package that parses multi BLAST results and returns them in a purpose-built object-database format. Unlike other BLAST parsers, BlaSTorage retains and stores all parts of BLAST results, including alignments, without loss of information; a complete API allows access to all the data components. Conclusions: BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.Pubblicat

The PARIGA server for real time filtering and analysis of reciprocal BLAST results

BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use

Pariga logical schema.

<p>Central columns represent the original input files, while results are indicated in the columns on the side. Boxes indicate logical operations that can be performed on the results. As an example: COMMON: which sequence(s) of the dataset B is(are) shared in BLAST results of sequence A2 and A3 of the dataset A? CROSS: once sequence A1 is selected from dataset A, in which results of the dataset B does it appear? MULTIPLE: which sequence of dataset A appears more than once (i.e. matches more than one region) in the results of sequence B2 of dataset B?</p

Real Time Filtering and Logical Operations. (Left) Real Time Filtering.

<p>Differently from other available tools, filtering of the returned results can be done in real time with PARIGA. By clicking the <i>filter</i> button, a form will appear where the user can insert the desired values (or ranges) and only filtered results will be shown. Four icons on the table header will show, from left to right, a graphical summary of the hits distribution on the query sequence, the results table, a Blast summary table and the Blast statistics. <b>(Right) Logical Operations.</b> The main result page will show three buttons that allow the user to perform logical operations between the two groups of results as described in the text.</p

Ammonium N-(pyridin-2-ylmethyl)oxamate (AmPicOxam): a novel precursor of calcium oxalate coating for carbonate stone substrates

Ammonium N-(pyridin-2-ylmethyl)oxamate (AmPicOxam), synthesized from O-methyl-N-(pyridin-2-ylmethyl)oxamate, was spectroscopically and structurally characterized and assayed as a novel precursor for the protection and consolidation of carbonate stone substrates. An in-depth characterization of treated and untreated biomicritic limestone and white Carrara marble samples was carried out by means of SEM microscopy, X-ray powder diffraction, helium pycnometry, determination of water transport properties, and pull-off tests. The improved solubility (1.00 M, 16.5% w/w) of the title compound with respect to ammonium oxalate (0.4 M, 5% w/w) results in the formation of a thicker protective coating of calcium oxalate (CaOx) dihydrate (weddellite) on marble and biomicrite samples after the treatment with 5% and 12% w/w water solutions, producing a reduction in the stone porosity and increased cohesion. Theoretical calculations were carried out at the DFT level to investigate both the electronic structure of the N-(pyridin-2-ylmethyl)oxamate anion and the hydrolysis reaction leading from AmPicOxam to CaOx.</p

Interobserver reproducibility of immunohistochemical HER-2/neu assessment in human breast cancer: An update from INQAT round III

The clinical interest in HER-2/neu is related to trastuzumab, a drug used to treat patients with invasive breast carcinoma overexpressing the HER-2/neu protein. It is very important to correctly identify those patients who may benefit from trastuzumab by accurate assessment of the HER-2/neu status. Of the various methods available, the Dako Herceptest for immunolhistochemical assay is considered the most reliable to reach this goal. The aim of this study was to investigate within a group of Italian laboratories the reproducibility of the results of HER-2/neu assessment by means of the Dako scoring system on slides stained with the Herceptest kit. This study was also conceived as the continuation of one of our previous studies, which was similar in its aims but different in the classification criteria adopted. Our results show that, whereas the intra-observer reproducibility was generally satisfactory, the interobserver reproducibility was not. Moreover, our findings confirm that the two extreme classes (0 and 3+) are more easy to identify than the other two and that the Herceptest does not allow to discriminate optimally between scoring classes 2+ and 3+. These findings are relevant in clinical practice where the treatment choice is based on categories defined by this assay, suggesting the need of adopting educational programs and/or new reference materials to improve the assay performance