panambioinfo.biology.gatech.edu
PanAmerican Bioinformatics Institute - Faculty
http://panambioinfo.biology.gatech.edu/studex.html
PABI faculty members host student exchanges between institutions in Latin America and the US. Jun - Jul 2016. Victoria M Caban Figueroa. Universidad de Puerto Rico, Río Piedras, PR. Host laboratory: King Jordan. Jan - Jun 2016. Universidad CES - EIA, Medellín, Colombia. Host laboratory: King Jordan. Jan - Jun 2015. Lina Andrea Alzate Rincón, Carlos Eduardo Tellez Villa. Universidad del Valle, Cali, Colombia. Host laboratory: King Jordan. Mar - Apr 2015. Lina C. Valderrama-Aguirre. Jan - Mar 2015. Februar...
enve-omics.ce.gatech.edu
Kostas lab | Data
http://enve-omics.ce.gatech.edu/data
This website contains links to publicly available data released by Kostas lab. See also: Publication from Kostas lab. And Research projects at Kostas lab. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Site developed by Luis M. Rodriguez-R.
enve-omics.ce.gatech.edu
Kostas lab | Tools
http://enve-omics.ce.gatech.edu/index
Environmental Microbial Genomics Laboratory. If you use the online tools in this website, please cite the article below and/or the article describing the specific algorithm/tool used (see corresponding webpages), as appropriate:. Rodriguez-R LM and Konstantinidis KT (2016). The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 4:e1900v1. The following list features some tools developed at Kostas lab:. ANI: Average Nucleotide Identity calculator.
enve-omics.ce.gatech.edu
Kostas lab | ANI calculator
http://enve-omics.ce.gatech.edu/ani
The ANI calculator estimates the average nucleotide identity using both best hits (one-way ANI) and reciprocal best hits (two-way ANI) between two genomic datasets, as calculated by Goris. Typically, the ANI values between genomes of the same species are above 95% (. Values below 75% are not to be trusted, and AAI. Should be used instead. This tool supports both complete and draft genomes (multi-fasta). For an introductory comment, see Rodriguez-R and Konstantinidis, 2014. How alignments are filtered.
enve-omics.ce.gatech.edu
Kostas lab | Nonpareil
http://enve-omics.ce.gatech.edu/nonpareil
Estimating coverage in metagenomes. Nonpareil uses the redundancy of the reads in a metagenomic dataset to estimate the average coverage and predict the ammount of sequences that will be required to achieve "nearly complete coverage", defined as ≥95% or ≥99% average coverage. You can use Nonpareil on-line. If you use Nonpareil, please cite:. On the importance of coverage estimations. Site developed by Luis M. Rodriguez-R.
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.
nenes.eas.gatech.edu
Nenes Group
http://nenes.eas.gatech.edu/NenesGroup/NenesGroup.html
Current Group and Alumni. Georgia Power Scholar, Cullen-Peck Fellow, Johnson Faculty Fellow. Schools of Earth and Atmospheric Sciences. And Chemical & Biomolecular Engineering. Georgia Institute of Technology. 311 Ferst Drive, Atlanta, GA 30332. ES&T 3258 (Office); ES&T 3155 (Lab). 1 (404) 894-9225 (Office); 1 (404) 894-5638 (Lab). Visiting Scholars and Affiliated Researchers. PhD in Chemistry, Environmental Chemical Processes Laboratory, University of Crete, Greece, 2009. BS in General Biology, Universi...
enve-omics.ce.gatech.edu
Kostas lab | ROCker
http://enve-omics.ce.gatech.edu/rocker
Accurately detecting functional genes in metagenomes. ROCker employs Receiver-Operator Curve (ROC)-analysis of. Generated metagenomic reads that map onto well-curated reference protein sequences, and a sliding window across the length of the reference sequences to deal with non-discriminative domains and motifs that are shared between functionally different proteins. You can download stand-alone ROCker. If you use ROCker, please cite:. Orellana LH, Rodriguez-R LM and Konstantinidis KT (.
enve-omics.ce.gatech.edu
Kostas lab | MyTaxa
http://enve-omics.ce.gatech.edu/mytaxa
Assign taxonomy to metagenomic fragments. MyTaxa represents a new algorithm that extends the Average Amino Acid Identity (AAI) concept ( Konstantinidis and Tiedje, PNAS 2005. To identify the taxonomic affiliation of a query genome sequence or a sequence of a contig assembled from a metagenome, including short sequences (. 100-1,000nt long), and to classify sequences representing novel taxa at three levels (whenever possible),. You can use MyTaxa on-line. Or download MyTaxa stand-alone.
