My Biosoftware – Bioinformatics Softwares Blog – Supply Bioinformatics Softwares Everyday

Time 2021-06-24 10:38:05

Web Name: My Biosoftware – Bioinformatics Softwares Blog – Supply Bioinformatics Softwares Everyday

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:: DESCRIPTIONDNAatGlance is a program for the detection of large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms.::DEVELOPERUA.PT Bioinformatics:: SCREENSHOTS:: REQUIREMENTSWindows / Linux:: DOWNLOAD DNAatGlance:: MORE INFORMATIONCitationPLoS One. 2013 Nov 21;8(11):e79922. doi: 10.1371/journal.pone.0079922. eCollection 2013.DNA sequences at a glance.Pinho AJ1, Garcia SP, Pratas D, Ferreira PJ.:: DESCRIPTIONNeji is a innovative and powerfull framework for faster biomedical concept recognition. It is open source and built around four key characteristics: modularity, scalability, speed, and usability. Neji integrates modules of various state-of-the-art methods for biomedical natural language processing (e.g., sentence splitting, tokenization, lemmatization, part-of-speech tagging, chunking and dependency parsing) and concept recognition (e.g., dictionaries and machine learning). The most popular input and output formats, such as Pubmed XML, IeXML, CoNLL and A1, are also supported.::DEVELOPERUA.PT Bioinformatics:: SCREENSHOTSN/A::REQUIREMENTSLinux/ Windows/MacOsX:: DOWNLOAD NEJI:: MORE INFORMATIONCitationBMC Bioinformatics. 2013 Sep 24;14:281. doi: 10.1186/1471-2105-14-281.A modular framework for biomedical concept recognition.Campos D1, Matos S, Oliveira JL.:: DESCRIPTIONbecas is a web application, API and widget for biomedical concept identification. It helps researchers, healthcare professionals and developers in the identification of over 1,200,000 biomedical concepts in text and PubMed abstracts.::DEVELOPERUA.PT Bioinformatics:: SCREENSHOTSN/A:: REQUIREMENTSWindows / Linux/ MacOsXPython:: DOWNLOAD BECAS API :: MORE INFORMATIONCitationBeCAS: biomedical concept recognition services and visualization.Nunes T, Campos D, Matos S, Oliveira JL.Bioinformatics. 2013 Aug 1;29(15):1915-6. doi: 10.1093/bioinformatics/btt317:: DESCRIPTIONEDSSI is an online bioinformatics pipeline that checks for syntax errors through three steps. First, ORF prediction in input DNA sequences is done by GeneMark; next, homologous sequences are retrieved by BLAST; and finally, syntax errors in the protein sequence are predicted by using the SIFT algorithm.:: DEVELOPERTim Hsiau:: SCREENSHOTSN/A:: REQUIREMENTSLinux / WindowsPython:: DOWNLOAD EDSSI:: MORE INFORMATIONCitationACS Synth Biol. 2014 Feb 21;3(2):91-6. doi: 10.1021/sb400176e. Epub 2014 Jan 3.Engineered DNA sequence syntax inspector.Hsiau TH1, Anderson JC.:: DESCRIPTIONMFCompress is a compression tool for FASTA and multi-FASTA files. In comparison to gzip and applied to multi-FASTA files, MFCompress can provide additional average compression gains of almost 50%, i.e.,it potentially doubles the available storage, although at the cost of some more computation time.::DEVELOPERUA.PT Bioinformatics:: SCREENSHOTS N/A:: REQUIREMENTSWindows / Linux:: DOWNLOAD MFCompress:: MORE INFORMATIONCitationArmando J. Pinho, and Diogo Pratas.“MFCompress: a compression tool for FASTA and multi-FASTA data.”Bioinformatics 30.1 (2014): 117-118.DOI: dx.doi.org/10.1093/bioinformatics/btt594.:: DESCRIPTIONARGminer is an online resource for the inspection and curation of ARGs based on crowdsourcing as well as a platform to promote interaction and collaboration for the ARG scientific community.::DEVELOPERProfessor Zhang Liqing’s Lab:: SCREENSHOTSN/A:: REQUIREMENTSWeb browser:: DOWNLOAD NO:: MORE INFORMATIONCitationArango-Argoty GA, Guron GKP, Garner E, Riquelme MV, Heath LS, Pruden A, Vikesland PJ, Zhang L.ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes.Bioinformatics. 2020 May 1;36(9):2966-2973. doi: 10.1093/bioinformatics/btaa095. PMID: 32058567.:: DESCRIPTIONDeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.::DEVELOPERProfessor Zhang Liqing’s Lab:: SCREENSHOTSN/A:: REQUIREMENTSLinuxPython:: DOWNLOAD DeepMicro:: MORE INFORMATIONCitationOh M, Zhang L.DeepMicro: deep representation learning for disease prediction based on microbiome data.Sci Rep. 2020 Apr 7;10(1):6026. doi: 10.1038/s41598-020-63159-5. PMID: 32265477; PMCID: PMC7138789.:: DESCRIPTIONNanoARG is an free web resource for the analysis of antibiotic resistance genes in metagenomes from environmental samples using the MinION nanopore sequencing technology.::DEVELOPERProfessor Zhang Liqing’s Lab:: SCREENSHOTSN/A:: REQUIREMENTSWeb browser:: DOWNLOAD NO:: MORE INFORMATIONCitationArango-Argoty GA, Dai D, Pruden A, Vikesland P, Heath LS, Zhang L.NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes.Microbiome. 2019 Jun 7;7(1):88. doi: 10.1186/s40168-019-0703-9. PMID: 31174603; PMCID: PMC6555988.:: DESCRIPTIONMetaCompare is a computational pipeline for prioritizing resistome risk by estimating the potential for ARGs to be disseminated into human pathogens from a given environmental sample based on metagenomic sequencing data.::DEVELOPERProfessor Zhang Liqing’s Lab:: SCREENSHOTSN/A:: REQUIREMENTSLinuxPython:: DOWNLOAD MetaCompare:: MORE INFORMATIONCitationOh M, Pruden A, Chen C, Heath LS, Xia K, Zhang L.MetaCompare: a computational pipeline for prioritizing environmental resistome risk.FEMS Microbiol Ecol. 2018 Jul 1;94(7):fiy079. doi: 10.1093/femsec/fiy079. PMID: 29718191; PMCID: PMC5995210.:: DESCRIPTIONBFAST-Gap is a modification of the BFAST short DNA read trimmer. BFAST-Gap adds functionality for Ion Torrent DNA reads.BisPin is a Python 2.7 program that uses BFAST-Gap (or BFAST) to map bisulfite-treated short DNA reads to a reference genome. It supports the hairpin construction strategy and rescores ambiguously mapped reads. Its default alignment scoring function is biologically motivated.::DEVELOPERProfessor Zhang Liqing’s Lab:: SCREENSHOTSN/A:: REQUIREMENTSLinuxPython:: DOWNLOAD BisPin:: MORE INFORMATIONCitationBisPin and BFAST-Gap: Mapping Bisulfite-Treated ReadsJacob Porter, Liqing ZhangbioRxiv 284596; doi: https://doi.org/10.1101/284596

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