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181 lines
8.8 KiB
BibTeX
181 lines
8.8 KiB
BibTeX
@article{cock2010sanger,
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title={The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants},
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author={Cock, Peter JA and Fields, Christopher J and Goto, Naohisa and Heuer, Michael L and Rice, Peter M},
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journal={Nucleic acids research},
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volume={38},
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number={6},
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pages={1767--1771},
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year={2010},
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publisher={Oxford University Press}
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}
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@ARTICLE{Boyer2016-gq,
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title = "{obitools: a unix-inspired software package for DNA metabarcoding}",
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author = "Boyer, Fr{\'e}d{\'e}ric and Mercier, C{\'e}line and Bonin,
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Aur{\'e}lie and Le Bras, Yvan and Taberlet, Pierre and Coissac,
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Eric",
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abstract = "DNA metabarcoding offers new perspectives in biodiversity
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research. This recently developed approach to ecosystem study
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relies heavily on the use of next-generation sequencing (NGS)
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and thus calls upon the ability to deal with huge sequence data
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sets. The obitools package satisfies this requirement thanks to
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a set of programs specifically designed for analysing NGS data
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in a DNA metabarcoding context. Their capacity to filter and
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edit sequences while taking into account taxonomic annotation
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helps to set up tailor-made analysis pipelines for a broad range
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of DNA metabarcoding applications, including biodiversity
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surveys or diet analyses. The obitools package is distributed as
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an open source software available on the following website:
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http://metabarcoding.org/obitools. A Galaxy wrapper is available
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on the GenOuest core facility toolshed:
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http://toolshed.genouest.org.",
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journal = "Molecular ecology resources",
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publisher = "Wiley Online Library",
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volume = 16,
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number = 1,
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pages = "176--182",
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month = jan,
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year = 2016,
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url = "http://dx.doi.org/10.1111/1755-0998.12428",
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keywords = "PCR errors; biodiversity; next-generation sequencing; sequence
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analysis; taxonomic annotation",
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language = "en",
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issn = "1755-098X, 1755-0998",
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pmid = "25959493",
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doi = "10.1111/1755-0998.12428"
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}
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@article{Lipman1985-hw,
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abstract = {An algorithm was developed which facilitates the search for
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similarities between newly determined amino acid sequences and
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sequences already available in databases. Because of the
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algorithm's efficiency on many microcomputers, sensitive protein
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database searches may now become a routine procedure for
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molecular biologists. The method efficiently identifies regions
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of similar sequence and then scores the aligned identical and
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differing residues in those regions by means of an amino acid
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replacability matrix. This matrix increases sensitivity by giving
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high scores to those amino acid replacements which occur
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frequently in evolution. The algorithm has been implemented in a
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computer program designed to search protein databases very
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rapidly. For example, comparison of a 200-amino-acid sequence to
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the 500,000 residues in the National Biomedical Research
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Foundation library would take less than 2 minutes on a
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minicomputer, and less than 10 minutes on a microcomputer (IBM
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PC).},
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author = {Lipman, D J and Pearson, W R},
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date-added = {2023-01-26 15:17:10 +0100},
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date-modified = {2023-01-26 15:17:10 +0100},
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issn = {0036-8075},
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journal = {Science},
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month = mar,
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number = 4693,
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pages = {1435--1441},
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pmid = {2983426},
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title = {{Rapid and sensitive protein similarity searches}},
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url = {http://www.ncbi.nlm.nih.gov/pubmed/2983426},
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volume = 227,
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year = 1985,
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bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/2983426}}
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@ARTICLE{Shehzad2012-pn,
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title = "{Carnivore diet analysis based on next-generation sequencing:
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Application to the leopard cat (Prionailurus bengalensis) in
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Pakistan}",
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author = "Shehzad, Wasim and Riaz, Tiayyba and Nawaz, Muhammad A and
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Miquel, Christian and Poillot, Carole and Shah, Safdar A and
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Pompanon, Francois and Coissac, Eric and Taberlet, Pierre",
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journal = "Molecular ecology",
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publisher = "Wiley Online Library",
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volume = 21,
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number = 8,
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pages = "1951--1965",
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year = 2012,
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url = "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x",
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issn = "0962-1083"
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}
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@ARTICLE{Riaz2011-gn,
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title = "{ecoPrimers: inference of new DNA barcode markers from whole
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genome sequence analysis}",
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author = "Riaz, Tiayyba and Shehzad, Wasim and Viari, Alain and Pompanon,
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Fran{\c c}ois and Taberlet, Pierre and Coissac, Eric",
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abstract = "Using non-conventional markers, DNA metabarcoding allows
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biodiversity assessment from complex substrates. In this article,
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we present ecoPrimers, a software for identifying new barcode
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markers and their associated PCR primers. ecoPrimers scans whole
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genomes to find such markers without a priori knowledge.
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ecoPrimers optimizes two quality indices measuring taxonomical
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range and discrimination to select the most efficient markers
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from a set of reference sequences, according to specific
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experimental constraints such as marker length or specifically
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targeted taxa. The key step of the algorithm is the
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identification of conserved regions among reference sequences for
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anchoring primers. We propose an efficient algorithm based on
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data mining, that allows the analysis of huge sets of sequences.
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We evaluate the efficiency of ecoPrimers by running it on three
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different sequence sets: mitochondrial, chloroplast and bacterial
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genomes. Identified barcode markers correspond either to barcode
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regions already in use for plants or animals, or to new potential
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barcodes. Results from empirical experiments carried out on a
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promising new barcode for analyzing vertebrate diversity fully
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agree with expectations based on bioinformatics analysis. These
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tests demonstrate the efficiency of ecoPrimers for inferring new
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barcodes fitting with diverse experimental contexts. ecoPrimers
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is available as an open source project at:
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http://www.grenoble.prabi.fr/trac/ecoPrimers.",
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journal = "Nucleic acids research",
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volume = 39,
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number = 21,
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pages = "e145",
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month = nov,
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year = 2011,
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url = "http://dx.doi.org/10.1093/nar/gkr732",
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language = "en",
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issn = "0305-1048, 1362-4962",
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pmid = "21930509",
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doi = "10.1093/nar/gkr732",
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pmc = "PMC3241669"
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}
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@ARTICLE{Seguritan2001-tg,
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title = "{FastGroup: a program to dereplicate libraries of 16S rDNA
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sequences}",
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author = "Seguritan, V and Rohwer, F",
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abstract = "BACKGROUND: Ribosomal 16S DNA sequences are an essential tool for
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identifying and classifying microbes. High-throughput DNA
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sequencing now makes it economically possible to produce very
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large datasets of 16S rDNA sequences in short time periods,
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necessitating new computer tools for analyses. Here we describe
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FastGroup, a Java program designed to dereplicate libraries of
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16S rDNA sequences. By dereplication we mean to: 1) compare all
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the sequences in a data set to each other, 2) group similar
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sequences together, and 3) output a representative sequence from
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each group. In this way, duplicate sequences are removed from a
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library. RESULTS: FastGroup was tested using a library of
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single-pass, bacterial 16S rDNA sequences cloned from
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coral-associated bacteria. We found that the optimal strategy for
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dereplicating these sequences was to: 1) trim ambiguous bases
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from the 5' end of the sequences and all sequence 3' of the
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conserved Bact517 site, 2) match the sequences from the 3' end,
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and 3) group sequences > or =97\% identical to each other.
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CONCLUSIONS: The FastGroup program simplifies the dereplication
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of 16S rDNA sequence libraries and prepares the raw sequences for
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subsequent analyses.",
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journal = "BMC bioinformatics",
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volume = 2,
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pages = "9",
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month = oct,
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year = 2001,
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url = "http://dx.doi.org/10.1186/1471-2105-2-9",
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language = "en",
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issn = "1471-2105",
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pmid = "11707150",
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doi = "10.1186/1471-2105-2-9",
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pmc = "PMC59723"
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}
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