A flexible ChIP-sequencing simulation toolkit

Συγγραφείς: Zheng, An, Lamkin, Michael, Qiu, Yutong, Ren, Kevin, Goren, Alon, Gymrek, Melissa

Πηγή: BMC Bioinformatics. 22(1)

Θεματικοί όροι: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), 3105 Genetics (for-2020), Genetics (rcdc), Human Genome (rcdc), Networking and Information Technology R&D (NITRD) (rcdc), Chromatin Immunoprecipitation Sequencing (mesh), Computer Simulation (mesh), Genome (mesh), High-Throughput Nucleotide Sequencing (mesh), Models, Statistical (mesh), Sequence Analysis, DNA (mesh), Software (mesh), Bioinformatics, Epigenomics, ChIP-sequencing, Simulation tool, Command-line program, Models, Statistical (mesh), Sequence Analysis, DNA (mesh), Genome (mesh), Computer Simulation (mesh), Software (mesh), High-Throughput Nucleotide Sequencing (mesh), Chromatin Immunoprecipitation Sequencing (mesh), Bioinformatics, ChIP-sequencing, Command-line program, Epigenomics, Simulation tool, Chromatin Immunoprecipitation Sequencing (mesh), Computer Simulation (mesh), Genome (mesh), High-Throughput Nucleotide Sequencing (mesh), Models, Statistical (mesh), Sequence Analysis, DNA (mesh), Software (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/39r2b3b7
https://escholarship.org/content/qt39r2b3b7/qt39r2b3b7.pdf

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files

Συγγραφείς: Altinkaya, Isin, Nielsen, Rasmus, Korneliussen, Thorfinn Sand

Πηγή: Bioinformatics. 41(4)

Θεματικοί όροι: 46 Information and Computing Sciences (for-2020), 31 Biological Sciences (for-2020), 4601 Applied Computing (for-2020), 3105 Genetics (for-2020), Bioengineering (rcdc), Genetics (rcdc), Networking and Information Technology R&D (NITRD) (rcdc), Biotechnology (rcdc), Human Genome (rcdc), Software (mesh), Genotype (mesh), Likelihood Functions (mesh), High-Throughput Nucleotide Sequencing (mesh), Computer Simulation (mesh), Humans (mesh), Computational Biology (mesh), Sequence Analysis, DNA (mesh), Humans (mesh), Likelihood Functions (mesh), Sequence Analysis, DNA (mesh), Computational Biology (mesh), Genotype (mesh), Computer Simulation (mesh), Software (mesh), High-Throughput Nucleotide Sequencing (mesh), Software (mesh), Genotype (mesh), Likelihood Functions (mesh), High-Throughput Nucleotide Sequencing (mesh), Computer Simulation (mesh), Humans (mesh), Computational Biology (mesh), Sequence Analysis, DNA (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/42f4g4w6
https://escholarship.org/content/qt42f4g4w6/qt42f4g4w6.pdf

Interactive computer programs for the graphic analysis of nucleotide sequence data.

Συγγραφείς: Luckow VA, Littlewood RK, Rownd RH

Πηγή: Nucleic acids research [Nucleic Acids Res] 1984 Jan 11; Vol. 12 (1 Pt 2), pp. 665-73.

Τύπος έκδοσης: Journal Article; Research Support, U.S. Gov't, P.H.S.

Στοιχεία περιοδικού: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Print ISSN: 0305-1048 (Print) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Base Sequence* , Computers* , Microcomputers* , Plasmids* , Software*, DNA/*genetics, Proteins/genetics ; Amino Acid Sequence ; Methods ; Nucleic Acid Conformation

Computer Program for Primer Design for Loop-Mediated Isothermal Amplification (LAMP)

Συγγραφείς: L. U. Akhmetzianov

Πηγή: Advanced Engineering Research, Vol 24, Iss 1, Pp 98-108 (2024)

Θεματικοί όροι: design, loop primers, python, с++, loop-mediated isothermal amplification, lamp, Materials of engineering and construction. Mechanics of materials, TA401-492

Περιγραφή αρχείου: electronic resource

Relation: https://www.vestnik-donstu.ru/jour/article/view/2163; https://doaj.org/toc/2687-1653

Σύνδεσμος πρόσβασης: https://doaj.org/article/759d31f4f863495eae04bf5d1365b261

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer.

Συγγραφείς: Burnett L; Department of Clinical Biochemistry, Royal Prince Alfred Hospital, Camperdown, NSW, Australia., Basten A, Hensley WJ

Πηγή: Computer applications in the biosciences : CABIOS [Comput Appl Biosci] 1985 Dec; Vol. 1 (4), pp. 241-7.

Τύπος έκδοσης: Journal Article; Research Support, Non-U.S. Gov't

Στοιχεία περιοδικού: Publisher: Oxford University Press Country of Publication: England NLM ID: 8511758 Publication Model: Print Cited Medium: Print ISSN: 0266-7061 (Print) Linking ISSN: 02667061 NLM ISO Abbreviation: Comput Appl Biosci Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Base Sequence* , Computers* , Microcomputers* , Minicomputers* , Software* , Software Design*, Algorithms

IonCRAM: a reference-based compression tool for ion torrent sequence files

Συγγραφείς: Shokrof, Moustafa, Abouelhoda, Mohamed

Πηγή: BMC Bioinformatics. 21(1)

Θεματικοί όροι: Information and Computing Sciences, Biological Sciences, Bioinformatics and Computational Biology, Bioengineering, Genetics, Human Genome, Algorithms, Databases, Genetic, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, User-Computer Interface, Mathematical Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/0g3707bv
https://escholarship.org/content/qt0g3707bv/qt0g3707bv.pdf

RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets

Συγγραφείς: Martin, Darren P, primary, Varsani, Arvind, additional, Roumagnac, Philippe, additional, Botha, Gerrit, additional, Maslamoney, Suresh, additional, Schwab, Tiana, additional, Kelz, Zena, additional, Kumar, Venkatesh, additional, Murrell, Ben, additional

Πηγή: Virus Evolution. 2020/04/12

Σύνδεσμος πρόσβασης: https://academic.oup.com/ve/advance-article-pdf/doi/10.1093/ve/veaa087/34696275/veaa087.pdf

CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases

Συγγραφείς: Grillo, Giorgio, primary, Attimonelli, Marcella, additional, Liuni, Sabino, additional, Pesole, Graziano, additional

Πηγή: Bioinformatics. 1996/01/01

Characteristic Features of the Nucleotide Sequences of Yeast Mitochondrial Ribosomal Protein Genes as Analyzed by Computer Program GeneMark

Συγγραφείς: Isono, K., primary

Πηγή: DNA Research. 1994/01/01

Σύνδεσμος πρόσβασης: https://academic.oup.com/dnaresearch/article-pdf/1/6/263/6935386/dnares_1_6_263.pdf

A personal computer program for large-scale comparisons of related nucleotide sequences

Συγγραφείς: Schipper, R., primary, Kenter, M., additional, de Wit, T.Rinke, additional, D‘Amaro, J., additional

Πηγή: Bioinformatics. 1992/01/01

The MTX package of computer programmes for the comparison of sequences of nucleotides and amino acid residues

Συγγραφείς: Reisner, A.H., primary, Bucholtz, C.A., additional

Πηγή: Nucleic Acids Research. 1986/01/01

Σύνδεσμος πρόσβασης: https://academic.oup.com/nar/article-pdf/14/1/233/7068542/14-1-233.pdf

ATAV: a comprehensive platform for population-scale genomic analyses

Συγγραφείς: Ren, Zhong, Povysil, Gundula, Hostyk, Joseph A., Cui, Hongzhu, Bhardwaj, Nitin, Goldstein, David B.

Θεματικοί όροι: Genomics, Nucleotide sequence--Computer programs, Nucleotide sequence--Computer network resources

Διαθεσιμότητα: https://doi.org/10.7916/yaa2-qy53

Microcomputer programs for prediction and comparative evaluation of protein secondary structure from nucleotide sequence data: application to ribulose-1,5-bisphosphate carboxylase sequences.

Συγγραφείς: Pongor S, Guttieri MJ, Cohen LM, Szalay AA

Πηγή: DNA (Mary Ann Liebert, Inc.) [DNA] 1985 Aug; Vol. 4 (4), pp. 319-26.

Τύπος έκδοσης: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Στοιχεία περιοδικού: Publisher: Mary Ann Liebert Country of Publication: United States NLM ID: 8302432 Publication Model: Print Cited Medium: Print ISSN: 0198-0238 (Print) Linking ISSN: 01980238 NLM ISO Abbreviation: DNA Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Computers* , Ribulose-Bisphosphate Carboxylase*, Base Sequence ; Epitopes ; Genes ; Hydrogen Bonding ; Protein Conformation ; Solubility

ATAV: a comprehensive platform for population-scale genomic analyses

Συγγραφείς: Zhong Ren, Gundula Povysil, Joseph A. Hostyk, Hongzhu Cui, Nitin Bhardwaj, David B. Goldstein

Πηγή: BMC Bioinformatics
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-15 (2021)

Θεματικοί όροι: Gene discovery, QH301-705.5, Nucleotide sequence--Computer programs, Computer applications to medicine. Medical informatics, Nucleotide sequence--Computer network resources, R858-859.7, Reproducibility of Results, Genome analysis, Genomics, Association testing, Genetics, Population, Phenotype, Databases, Genetic, Exome Sequencing, Humans, Diagnostic, Biology (General), Web platform, Software

Σύνδεσμος πρόσβασης: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04071-1
https://pubmed.ncbi.nlm.nih.gov/33757430
https://doaj.org/article/634b91bd94b8499f91cd4d8b3081f9c3

Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences

Συγγραφείς: Nagel, Anna A, Flouri, Tomáš, Yang, Ziheng, Rannala, Bruce

Πηγή: Systematic Biology. 73(6)

Θεματικοί όροι: Biological Sciences, Evolutionary Biology, Genetics, Bioengineering, DNA, Ancient, Animals, Bayes Theorem, Phylogeny, Classification, Mammoths, Elephants, Models, Genetic, Computer Simulation, aDNA, BPP, multispecies coalescent, tip dating, Ecology, Evolutionary biology

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/2ps0b99k
https://escholarship.org/content/qt2ps0b99k/qt2ps0b99k.pdf

Detection of microRNAs in color space.

Συγγραφείς: Marco, Antonio, Griffiths-Jones, Sam

Πηγή: Bioinformatics; Feb2012, Vol. 28 Issue 3, p318-323, 6p

Θεματικοί όροι: RNA analysis, Color, Nucleotide sequence, Linkers (Computer programs), Genetic transcription, Genetic polymorphisms, Computational biology

Probabilistic machine learning for predictions and causal discovery in health informatics.

Συγγραφείς: Nazaret, Achille Oscar Romeo

Θεματικοί όροι: Artificial intelligence, Medical sciences, Bioinformatics, Machine learning, Medical informatics, Health--Information services, Medicine--Information technology, Probabilities--Computer programs, Genomics, Nucleotide sequence--Computer programs, Acute myeloid leukemia

Διαθεσιμότητα: https://doi.org/10.7916/2fse-kv24

PEAS V1.0: a package for elementary analysis of SNP data.

Συγγραφείς: SHUHUA XU^1,2 xushua@picb.ac.cn, GUPTA, SANCHIT¹, LI JIN^1,2,3,4 ljin007@gmail.com

Πηγή: Molecular Ecology Resources. Nov2010, Vol. 10 Issue 6, p1085-1088. 4p. 1 Chart.

Θεματικοί όροι: *Computer software, *Nucleotide sequence, *Genetics, *Molecular phylogeny, *Molecular evolution

Representation Learning for CRISPR-Cas13d Efficacy and Single-Cell RNA Sequencing Data

Συγγραφείς: Stirn, Andrew

Θεματικοί όροι: Artificial intelligence, Machine learning, Nucleotide sequence--Computer programs, RNA, CRISPR (Genetics), Genomics

Διαθεσιμότητα: https://doi.org/10.7916/c1gh-7403

Observer agreement for event sequences: Methods and software for sequence alignment and reliability estimates.

Συγγραφείς: Quera, Vicenç, Bakeman, Roger, Gnisci, Augusto

Πηγή: Behavior Research Methods; Feb2007, Vol. 39 Issue 1, p39-49, 11p, 3 Diagrams, 2 Charts, 4 Graphs

Θεματικοί όροι: Chronology, Statistics, Nucleotide sequence, Simulation methods & models, Computer software, Algorithms