The Bologna Annotation Resource: a Non Hierarchical Method for the Functional and Structural Annotation of Protein Sequences Relying on a Comparative Large-Scale Genome Analysis

2009 ◽  
Vol 8 (9) ◽  
pp. 4362-4371 ◽  
Author(s):  
Lisa Bartoli ◽  
Ludovica Montanucci ◽  
Raffaele Fronza ◽  
Pier Luigi Martelli ◽  
Piero Fariselli ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Large Scale ◽  
Protein Sequences ◽  
Structural Annotation ◽  
Hierarchical Method

scholarly journals PaperBLAST: Text-mining papers for information about homologs

2017 ◽  
Author(s):  
Morgan N. Price ◽  
Adam P. Arkin
Keyword(s):  
Text Mining ◽  
Genome Sequencing ◽  
Full Text ◽  
Large Scale ◽  
Scientific Literature ◽  
Protein Sequences ◽  
Protein Coding ◽  
Link Protein ◽  
Protein Coding Genes ◽  
Link Type

AbstractLarge-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/.

scholarly journals Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

GigaScience ◽  
2018 ◽  
Vol 7 (4) ◽  
Author(s):  
Harry A Thorpe ◽  
Sion C Bayliss ◽  
Samuel K Sheppard ◽  
Edward J Feil
Keyword(s):  
Genome Analysis ◽  
Large Scale ◽  
Analysis Tool ◽  
Pan Genome ◽  
Intergenic Regions

Analysis of Large-Scale Human Protein Sequences Using an Efficient Spark-Based DBSCAN Algorithm

2020 ◽  
pp. 601-609
Author(s):  
Soumyendu Sekhar Bandyopadhyay ◽  
Anup Kumar Halder ◽  
Piyali Chatterjee ◽  
Jacek Sroka ◽  
Mita Nasipuri ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Sequences ◽  
Human Protein ◽  
Dbscan Algorithm

An alternative to radiation hybrid mapping for large-scale genome analysis in barley

2005 ◽  
Vol 274 (6) ◽  
pp. 589-594 ◽  
Author(s):  
Ali Masoudi-Nejad ◽  
Shuhei Nasuda ◽  
Marie-Therese Bihoreau ◽  
Robbie Waugh ◽  
Takashi Ryu Endo
Keyword(s):  
Genome Analysis ◽  
Radiation Hybrid ◽  
Large Scale ◽  
Radiation Hybrid Mapping ◽  
Hybrid Mapping

RECOGNITION OF TRANSMEMBRANE SEGMENTS IN PROTEINS: REVIEW AND CONSISTENCY-BASED BENCHMARKING OF INTERNET SERVERS

2006 ◽  
Vol 04 (05) ◽  
pp. 1033-1056 ◽  
Author(s):  
NATALIYA S. SADOVSKAYA ◽  
ROMAN A. SUTORMIN ◽  
MIKHAIL S. GELFAND
Keyword(s):  
Membrane Proteins ◽  
Genome Annotation ◽  
Large Scale ◽  
Protein Sequences ◽  
Transmembrane Segments ◽  
Enzyme Complexes

Membrane proteins perform a number of crucial functions as transporters, receptors, and components of enzyme complexes. Identification of membrane proteins and prediction of their topology is thus an important part of genome annotation. We present here an overview of transmembrane segments in protein sequences, summarize data from large-scale genome studies, and report results of benchmarking of several popular internet servers.

scholarly journals Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing

2007 ◽  
Vol 8 (1) ◽  
pp. 396 ◽  
Author(s):  
Tobias Wittkop ◽  
Jan Baumbach ◽  
Francisco P Lobo ◽  
Sven Rahmann
Keyword(s):  
Large Scale ◽  
Protein Sequences ◽  
Cluster Editing

scholarly journals GIGGLE: a search engine for large-scale integrated genome analysis

2017 ◽  
Author(s):  
Ryan M. Layer ◽  
Brent S. Pedersen ◽  
Tonya DiSera ◽  
Gabor T. Marth ◽  
Jason Gertz ◽  
...  
Keyword(s):  
Data Integration ◽  
Search Engine ◽  
Genome Analysis ◽  
Large Scale ◽  
Hypothesis Generation ◽  
Link Type

AbstractGIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files. GIGGLE scales to billions of intervals, is faster (+1,000X) than existing methods, and its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEX by facilitating data integration and hypothesis generation. GIGGLE is available at https://github.com/ryanlayer/giggle.

scholarly journals Large-scale sequence comparisons with sourmash

2019 ◽  
Author(s):  
N. Tessa Pierce ◽  
Luiz Irber ◽  
Taylor Reiter ◽  
Phillip Brooks ◽  
C. Titus Brown
Keyword(s):  
Software Package ◽  
Large Scale ◽  
Sequence Similarity ◽  
Protein Sequences ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Sequence Comparisons ◽  
Large Databases ◽  
Scale Sequence

The sourmash software package uses MinHash-based sketching to create “signatures”, compressed representations of DNA, RNA, and protein sequences, that can be stored, searched, explored, and taxonomically annotated. sourmash signatures can be used to estimate sequence similarity between very large data sets quickly and in low memory, and can be used to search large databases of genomes for matches to query genomes and metagenomes. sourmash is implemented in C++, Rust, and Python, and is freely available under the BSD license at http://github.com/dib-lab/sourmash.

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