monarchbase.umassmed.edu
MonarchBase - Help
http://monarchbase.umassmed.edu/help.html
Browse genome using GBrowse. Query a single gene. Search a group of genes. Query ESTs and migratory profiles. Browse expanded and contracted gene families. Use the appropriate formats when searching data with IDs:. C1 or BF010 xxxxxxx. Go back to the menu. For BLAST, use sequences as input to search for monarch scaffolds, contigs, genes, ESTs, as well as proteins of other insect orders. Select the appropriate search programs and databases. Advanced users can also set the optional parameters. Of MonarchBa...
molbiol-tools.ca
Eukaryotic genes
http://www.molbiol-tools.ca/Eukarytoic_genes.htm
Because many genes in eukaryotes are interrupted by introns it can be difficult to identify the protein sequence of the gene. Furthermore, programs designed for recognizing intron/exon boundaries for a particular organism or group of organisms may not recognize all intron/exons boundaries. No single site should be used, rather a combinatorial approach should be taken, incorporating BLAST and the programs outlined below, when studying eukaryotic genes. DNA functional site miner. Is an updated version whic...
crdd.osdd.net
Computational tools for genome annotation
http://crdd.osdd.net/ga.php
Data on M.tb. Computaional Tools for Genome Annotation. Several computational tools have been developed to cut down time and expense involved in the experimental procedure of annotation. Computational resources at CRDD have been classified in following categories:. Servers integrated at CRDD. This server allows to predict gene (protein coding regions) in eukaryote genomes that includes introns and exons, using similarity aided (double) and consensus Ab Intion methods. (. It is a support vector based appr...
en.wikipedia.org
Earth Microbiome Project - Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Earth_Microbiome_Project
From Wikipedia, the free encyclopedia. The Earth Microbiome Project. EMP) is an initiative to collect natural samples and to analyze the microbial community around the globe. Are highly abundant, diverse, and have an important role in the ecological system. There are an estimated 1.3 10. Cells, 3.1 10. Cells, and 1 10. Particles in the ocean. The bacterial diversity, a measure of the number of types. Yet as of 2010. And the specific interactions between microbes are largely unknown. The primary goa...
molbiol-tools.ca
Online Analysis Tools - Translation
http://www.molbiol-tools.ca/Translation.htm
A number of excellent sites exist all of which permit translation in all six reading frames. I would recommend ORF Finder because of its visuals and Pipeline or GeneMark if you are seriously interested in identifying genes within your sequence. The latter two programs permit the analysis of long sequences (submit by attachment not in the box). Frameshift errors in DNA sequence - several sites are available. Genio/scan N. Mache). T Schliex et al. 2003. Nucl. Acids Res. 31:. Facilitates the identification ...
enve-omics.ce.gatech.edu
Kostas lab | AAI calculator
http://enve-omics.ce.gatech.edu/aai
Average Amino acid Identity. The AAI calculator estimates the average amino acid identity using both best hits (one-way AAI) and reciprocal best hits (two-way AAI) between two genomic datasets of proteins. For an introductory comment, see Rodriguez-R and Konstantinidis, 2014. Sequences as input; this tool does not. Predict protein-coding regions. If you want to compare genomic sequences instead, please use the ANI calculator. Your name, a valid e-mail address, and a name to identify the job.
crdd.imtech.res.in
Computational tools for genome annotation
http://crdd.imtech.res.in/ga.php
Data on M.tb. Computaional Tools for Genome Annotation. Several computational tools have been developed to cut down time and expense involved in the experimental procedure of annotation. Computational resources at CRDD have been classified in following categories:. Servers integrated at CRDD. This server allows to predict gene (protein coding regions) in eukaryote genomes that includes introns and exons, using similarity aided (double) and consensus Ab Intion methods. (. It is a support vector based appr...
compgenomics2009.biology.gatech.edu
Gene prediction group - Compgenomics 2009
http://www.compgenomics2009.biology.gatech.edu/index.php/Gene_prediction_group
Gene Prediction Final Presentation. Glimmer Release Notes 3.02. ELPH (RBS finder used in Glimmer3) User Manual. Gene Prediction on Wikipedia. Last Year's Gene Prediction Group. List of Gene finding softwares. Retrieved from " http:/ www.compgenomics2009.biology.gatech.edu/index.php/Gene prediction group. Log in / create account. This page was last modified 02:26, 23 April 2009. This page has been accessed 7,156 times.
oziasakinslab.org
Sequence Databases and Bioinformatics Tools | Ozias-Akins Biotechnology Laboratory
http://oziasakinslab.org/links/bioinformatics-tools
Plant Biotechnology: Peanut & Grasses. Education & Outreach. Sequence Databases and Bioinformatics Tools. Papers & Presentations. Sequence Databases and Bioinformatics Tools. Peggy Ozias-Akins The University of Georgia. First peanut genome sequenced. April 4, 2014. Proudly powered by WordPress.
quast.bioinf.spbau.ru
QUAST 4.4 manual
http://quast.bioinf.spbau.ru/manual.html
QUAST 4.4 manual. QUAST stands for QU. Ool The tool evaluates genome assemblies by computing various metrics. This document provides instructions for the general QUAST. Tool for genome assemblies, MetaQUAST. The extension for metagenomic datasets, and Icarus. Interactive visualizer for these tools. You can find all project news and the latest version of the tool at http:/ quast.sf.net/. An improvement over MUMmer. In addition, MetaQUAST uses MetaGeneMark. Also we use bedtools. Feedback and bug reports.
