Ncbi software

This site contains the trace chromatogram data organized by species. Data include chromatogram, quality scores, FASTA sequences from automatic base calls, and other ancillary information in tab-delimited text as well as XML formats. This site contains whole genome shotgun sequence data organized by the 4-digit project code. Data include GenBank and GenPept flat files, quality scores and summary statistics. Access to individual-level data, including phenotypic data tables and genotypes, requires varying levels of authorization.

A suite of tag sets for authoring and archiving journal articles as well as transferring journal articles from publishers to archives and between archives. There are four tag sets: Archiving and Interchange Tag Set - Created to enable an archive to capture as many of the structural and semantic components of existing printed and tagged journal material as conveniently as possible; Journal Publishing Tag Set - Optimized for archives that wish to regularize and control their content, not to accept the sequence and arrangement presented to them by any particular publisher; Article Authoring Tag Set - Designed for authoring new journal articles; NCBI Book Tag Set - Written specifically to describe volumes for the NCBI online libraries.

This service allows users to download compound or substance records corresponding to a set of PubChem identifiers, which can be supplied manually or through a text file.

An online form that provides an interface for researchers, consortia and organizations to register their BioProjects. This serves as the starting point for the submission of genomic and genetic data for the study. The data does not need to be submitted at the time of BioProject registration.

A web-based sequence submission tool for one or a few submissions to the GenBank database, designed to make the submission process quick and easy. Tool for submission to the GenBank database of Barcode short nucleotide sequences from a standard genetic locus for use in species identification. It is capable of handling simple submissions that contain a single short mRNA sequence, complex submissions containing long sequences, multiple annotations, segmented sets of DNA, as well as sequences from phylogenetic and population studies with alignments.

For simple submission, use the online submission tool BankIt instead. A command-line program that automates the creation of sequence records for submission to GenBank using many of the same functions as Sequin. It is used primarily for submission of complete genomes and large batches of sequences.

This site enables users to submit data to the PubChem Substance and BioAssay databases, including chemical structures, experimental biological activity results, annotations, siRNA data and more. It can also be used to update previously submitted records.

The SNP database tools page provides links to the general submission guidelines and to the submission handle request. The page has also two specific links for single- or batch submissions of the human variation data using Human Genome Variation Society nomenclature.

A single entry point for submitters to link to and find information about all of the data submission processes at NCBI. Future additions to this site are planned. This link describes how submitters of trace data can obtain a secure NCBI FTP site for their data, and also describes the allowed data formats and directory structures.

Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes. The default display provides ready navigation to review alignments in the Graphics display.

Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families. Allows you to retrieve records from many Entrez databases by uploading a file of GI or accession numbers from the Nucleotide or Protein databases, or a file of unique identifiers from other Entrez databases.

Search results can be saved in various formats directly to a local file on your computer. A stand-alone application for classifying protein sequences and investigating their evolutionary relationships. CDTree can import, analyze and update existing Conserved Domain CDD records and hierarchies, and also allows users to create their own.

Cn3D simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features. Identifies the conserved domains present in a protein sequence. Tools that provide access to data within NCBI's Entrez system outside of the regular web query interface. They provide a method of automating Entrez tasks within software applications. Each utility performs a specialized retrieval task, and can be used simply by writing a specially formatted URL.

This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool BLAST algorithm. NCBI's Remap tool allows users to project annotation data and convert locations of features from one genomic assembly to another or to RefSeqGene sequences through a base by base analysis. Options are provided to adjust the stringency of remapping, and summary results are displayed on the web page.

Full results can be downloaded for viewing in NCBI's Genome Workbench graphical viewer, and annotation data for the remapped features, as well as summary data, is also available for download. An integrated application for viewing and analyzing sequence data.

With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix these data with your own data. An interactive web application that enables users to visualize multiple alignments created by database search results or other software applications.

The MSA Viewer allows users to upload an alignment and set a master sequence, and to explore the data using features such as zooming and changing of coloration. A set of software and data exchange specifications used by NCBI to produce portable, modular software for molecular biology.

A public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat STR DNA profiles based on laboratory-specific protocols.

OSIRIS evaluates the raw electrophoresis data using an independently derived mathematically-based sizing algorithm. It offers two new peak quality measures - fit level and sizing residual. It can be customized to accommodate laboratory-specific signatures such as background noise settings, customized naming conventions and additional internal laboratory controls.

A graphical analysis tool that finds all open reading frames in a user's sequence or in a sequence already in the database. Sixteen different genetic codes can be used. The deduced amino acid sequence can be saved in various formats and searched against protein databases using BLAST. The potential products are then automatically analyzed with a BLAST search against user specified databases, to check the specificity to the target intended. A utility for computing alignment of proteins to genomic nucleotide sequence.

It is based on a variation of the Needleman Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, ProSplign is accurate in determining splice sites and tolerant to sequencing errors. PUG provides access to PubChem services via a programmatic interface. PUG allows users to download data, initiate chemical structure searches, standardize chemical structures and interact with the E-utilities.

Standardization, in PubChem terminology, is the processing of chemical structures in the same way used to create PubChem Compound records from contributors' original structures. In the design phase, considering the summed density of pixels in rows and columns of the images, the teeth were separated from each other and the unnecessary regions; for example, the root area in the alveolar bone was eliminated.

Therefore, based on summed intensities, each image was segmented such that each segment contained only one tooth. Subsequently, based on the fuzzy logic, a well-known data-clustering algorithm named fuzzy c-means FCM was applied to the images to cluster or segment each tooth.

This algorithm is referred to as a soft clustering method, which assigns data elements to one or more clusters with a specific membership function. Using the extracted clusters, the tooth border was determined and assessed for cavity. The results of histological analysis were used as the gold standard for comparison with the results obtained from the software. Depth of caries was measured, and finally Intraclass Correlation Coefficient ICC and Bland-Altman plot were used to show the agreement between the methods.

The ICC for detection of enamel caries between the computer software and histological analysis results was determined as 0. Bland-Altman plot showed an acceptable agreement for measuring the depth of caries in enamel and dentin.