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The UCSC Genome Browser.
Authors: Karolchik D, Hinrichs AS, Kent WJ Abstract The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation "tracks." The annotations-generated by the UCSC Genome Bioinformatics Group and external collaborators-display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Protein identification using Sorcerer 2 and SEQUEST.
Authors: Lundgren DH, Martinez H, Wright ME, Han DK Abstract Sage-N's Sorcerer 2 provides an integrated data analysis system for comprehensive protein identification and characterization. It runs on a proprietary version of SEQUEST(R), the most widely used search engine for identifying proteins in complex mixtures. The protocol presented here describes the basic steps performed to process mass spectrometric data with Sorcerer 2 and how to analyze results using TPP and Scaffold. The unit also provides an overview of the SEQUEST(R) algorithm, along with Sorcerer-SEQUEST(R) enhancements, and a discussion of d...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the Generic Genome Browser (GBrowse).
Authors: Donlin MJ Abstract A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. The Generic Genome Browser (GBrowse) is an open-source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002). GBrowse can be configured to display genomic sequence features for any organism and is the browser used for the model organisms Drosophila melanogaster (Grumbling and Strelets, 2006) and Caenorhabditis elegans (Schwarz et al., 2006), among others. The softwa...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the NCBI map viewer to browse genomic sequence data.
Authors: Wolfsberg TG Abstract This unit includes a Basic Protocol with an introduction to the Map Viewer, describing how to perform a simple text-based search of genome annotations to view the genomic context of a gene, navigate along a chromosome, zoom in and out, and change the displayed maps to hide and show information. It also describes some of NCBI's sequence-analysis tools, which are provided as links from the Map Viewer. The Alternate Protocols describe different ways to query the genome sequence, and also illustrate additional features of the Map Viewer. Alternate Protocol 1 shows how to perform ...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the DFCI gene index databases for biological discovery.
Authors: Antonescu C, Antonescu V, Sultana R, Quackenbush J Abstract The DFCI Gene Index Web pages provide access to analyses of ESTs and gene sequences for nearly 114 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a home page. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using fu...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

miRBase: microRNA sequences and annotation.
Authors: Griffiths-Jones S Abstract miRBase is the central repository for microRNA (miRNA) sequence information. miRBase has a role in defining the nomenclature for miRNA genes and assigning names to novel miRNAs for publication in peer-reviewed journals. The online miRBase database is a resource containing all published miRNA sequences, together with textual annotation and links to the primary literature and to other secondary databases. The database provides a variety of methods to query the data, by specific searches of sequences and associated text and literature. All miRBase data are also available fo...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Census for proteome quantification.
Authors: Park SK, Yates JR Abstract Quantitative analysis has become increasingly important in the proteomics field; however, the large amount of mass spectrometric data and the different types of quantitative strategies make data analysis ever challenging. Here we describe a quantitative software tool called Census to analyze high-throughput mass spectrometry data from shotgun proteomics experiments in an efficient way. Census is capable of analyzing various stable isotope labeling experiments (using, e.g., (15)N, (18)O, SILAC, iTRAQ, TMT) in addition to labeling-free experiments. With high-resolution dat...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Computing multiple sequence/structure alignments with the T-coffee package.
Authors: Notredame C Abstract In this unit, we describe assembly of a multiple sequence alignment using the T-Coffee package. T-Coffee is much more flexible than most related methods (e.g., ClustalW) because it makes it possible to combine many alternative alignments into a single one, based on an estimate of consistency between these alignments. This strategy can be especially useful when one has to decide among the output produced by several alternative methods. PMID: 20205190 [PubMed - indexed for MEDLINE] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes.
Authors: Lamesch P, Dreher K, Swarbreck D, Sasidharan R, Reiser L, Huala E Abstract The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, biochemical pathways, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are ...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the ensembl genome server to browse genomic sequence data.
Authors: Fernández-Suárez XM, Schuster MK Abstract The Ensembl project provides a comprehensive source of automatic annotation of the human genome sequence, as well as other species of biomedical interest, with confirmed gene predictions that have been integrated with external data sources. This unit describes how to use the Ensembl genome browser (http://www.ensembl.org/), the public interface of the project. It describes how to find a gene or protein of interest, how to get additional information and external links, and how to use the comparative genomic data. Curr. Protoc. Bioinform. 30:1.15.1-1.15.48...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

MultiPipMaker: a comparative alignment server for multiple DNA sequences.
Authors: Elnitski L, Burhans R, Riemer C, Hardison R, Miller W Abstract The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment and/or stacked, pairwise percent identity plots, and support for user-specified annotations of genomic features and...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Analyzing shotgun proteomic data with PatternLab for proteomics.
Authors: Carvalho PC, Yates Iii JR, Barbosa VC Abstract PatternLab for proteomics is a one-stop shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins/peptides that are differentially expressed and those that are unique to a state. It can also cluster the ones that share similar expression profiles in time-course experiments, as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface. PMID: 20521246 [PubMed - indexed for MEDLINE] (Source: Current Protoco...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Exploring zebrafish genomic, functional and phenotypic data using ZFIN.
Authors: Ramachandran S, Ruef B, Pich C, Sprague J Abstract The zebrafish model organism database (ZFIN) provides a Web resource of zebrafish genomic, genetic, developmental, and phenotypic data. ZFIN curates and integrates data from current literature and from direct data submissions from laboratories. In addition, ZFIN collaborates with other bioinformatics organizations to provide links to other relevant data. These data can be accessed through a variety of Web-based search and display tools. This unit focuses on some of the basic methods to search, visualize, and analyze ZFIN data, including genes, gen...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the Velvet de novo assembler for short-read sequencing technologies.
Authors: Zerbino DR Abstract The Velvet de novo assembler was designed to build contigs and eventually scaffolds from short-read sequencing data. This protocol describes how to use Velvet, interpret its output, and tune its parameters for optimal results. It also covers practical issues such as configuration, using the VelvetOptimiser routine, and processing colorspace data. PMID: 20836074 [PubMed - indexed for MEDLINE] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Predicting peptide retention times for proteomics.
Authors: Krokhin OV, Spicer V Abstract The vast majority of modern bottom-up proteomic protocols include chromatographic reversed-phase (RP) fractionation of peptides prior to mass-spectrometric analysis. Retention time information can be easily extracted from LC-MS data and it can be used to improve protein identification/characterization procedures. The key to the success of this procedure is the correct retention time prediction based on compositional and structural properties of the separated species. Our Sequence Specific Retention Calculator (SSRCalc) is a Web-based peptide retention prediction that ...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research