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Cited by 75Genomics and Phylogenetic StudiesGenomics and Rare DiseasesGenetics, Bioinformatics, and Biomedical Research

Management of High-Throughput DNA Sequencing Projects: Alpheus

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Andrew F, Neil AM·2008·Journal of Computer Science & Systems Biology
DOI 10.4172/jcsb.1000013PMC PMC2819532
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Abstract

High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multi-gigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem's SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.

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Research works printed but not linked: 40

  1. [1]Addo QC Eshoo TW Bartel DP Axtell MJ 2008 Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome Curr Biol 18 758 762 18472421 PMC2583427
  2. [2]Addo QC Miller W Axtell MJ 2008 CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets Bioinformatics (Oxford, England) PMC3202307 19017659
  3. [3]Altschul SF Madden TL Schaffer AA Zhang J Zhang Z 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic acids research 25 3389 3402 9254694 PMC146917
  4. [4]Burnside J Ouyang M Anderson A Bernberg E Lu C 2008 Deep sequencing of chicken microRNAs BMC genomics 9 185 18430245 PMC2375912
  5. [5]Butcher LM Beck S 2008 Future impact of integrated high-throughput methylome analyses on human health and disease Journal of genetics and genomics = Yi chuan xue bao 35 391 401 18640619
  6. [6]Chellappan P Jin H 2009 Discovery of Plant MicroRNAs and Short-Interfering RNAs by Deep Parallel Sequencing Methods in molecular biology (Clifton, NJ) 495 1 12 19085152
  7. [7]Craig DW Pearson JV Szelinger S Sekar A Redman M 2008 Identification of genetic variants using bar-coded multiplexed sequencing Nature methods 5 887 893 18794863 PMC3171277
  8. [8]Flicek P Aken BL Beal K Ballester B Caccamo M 2008 Ensembl 2008 Nucleic acids research 36 D707 714 18000006 PMC2238821
  9. [9]German MA Pillay M Jeong DH Hetawal A Luo S 2008 Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends Nature biotechnology 26 941 946 18542052
  10. [10]Goossens D Moens LN Nelis E Lenaerts AS Glassee W 2008 Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing Human mutation 19058222
  11. [11]Hafner M Landgraf P Ludwig J Rice A Ojo T 2008 Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing Methods (San Diego Calif) 44 3 12 PMC2847350 18158127
  12. [12]Henikoff S Henikoff JG 1993 Performance evaluation of amino acid substitution matrices Proteins 17 49 61 8234244
  13. [13]Hillier LW Marth GT Quinlan AR Dooling D Fewell G 2008 Whole-genome sequencing and variant discovery in C. elegans Nature methods 5 183 188 18204455
  14. [14]Kunin V Copeland A Lapidus A Mavromatis K Hugenholtz P 2008 A bioinformatician’s guide to metagenomics Microbiol Mol Biol Rev 72 557 578 19052320 PMC2593568
  15. [15]Lister R O’Malley RC Tonti FJ Gregory BD Berry CC 2008 Highly integrated single-base resolution maps of the epigenome in Arabidopsis Cell 133 523 536 18423832 PMC2723732
  16. [16]Lu C Jeong DH Kulkarni K Pillay M Nobuta K 2008 Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs) Proceedings of the National Academy of Sciences of the United States of America 105 4951 4956 18353984 PMC2290808
  17. [17]Lu C Kulkarni K Souret FF MuthuValliappan R Tej SS 2006 MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA poly-merase-2 mutant Genome research 16 1276 1288 16954541 PMC1581437
  18. [18]Lu C Meyers BC Green PJ 2007 Construction of small RNA cDNA libraries for deep sequencing Methods (San Diego, Calif) 43 110 117 17889797
  19. [19]Mangan ME Williams JM Lathe SM Karolchik D Lathe WC 3rd 2008 UCSC genome browser: deep support for molecular biomedical research Biotechnology annual review 14 63 108 18606360
  20. [21]Mardis ER 2008 The impact of next-generation sequencing technology on genetics Trends Genet 24 133 141 18262675
  21. [22]Marioni JC Mason CE Mane SM Stephens M Gilad Y 2008 RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays Genome research 18 1509 1517 18550803 PMC2527709
  22. [23]Medini D Serruto D Parkhill J Relman DA Donati C 2008 Microbiology in the post-genomic era Nat Rev Microbiol 6 419 430 18475305
  23. [24]Morozova O Marra MA 2008 From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors Biochemistry and cell biology = Biochimie et biologie cellulaire 86 81 91 18443621
  24. [25]Mortazavi A Williams BA McCue K Schaeffer L Wold B 2008 Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature methods 5 621 628 18516045 PMC13303166
  25. [26]Mudge J Miller NA Khrebtukova I Lindquist IE May GD 2008 Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum PLoS ONE 3 e3625 18985160 PMC2576459
  26. [27]Nagalakshmi U Wang Z Waern K Shou C Raha D Gerstein M 2008 The transcriptional landscape of the yeast genome defined by RNA sequencing Science (New York, N.Y) 320 1344 1349 PMC2951732 18451266
  27. [28]Pan Q Shai O Lee LJ Frey BJ Blencowe BJ 2008 Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing Nature genetics 40 1413 1415 18978789
  28. [29]Pomraning KR Smith KM Freitag M 2008 Genome-wide high throughput analysis of DNA methylation in eukaryotes Methods (San Diego, Calif) 18950712
  29. [30]Pruitt KD Tatusova T Maglott DR 2005 NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic acids research 33 D501 504 15608248 PMC539979
  30. [31]Ramensky V Bork P Sunyaev S 2002 Human non-synonymous SNPs: server and survey Nucleic acids research 30 3894 3900 12202775 PMC137415
  31. [32]Ropers HH 2007 New perspectives for the elucidation of genetic disorders American journal of human genetics 81 199 207 17668371 PMC1950818
  32. [33]Shin H Hirst M Bainbridge MN Magrini V Mardis E 2008 Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags BMC biology 6 30 18611272 PMC2474577
  33. [34]Siva N 2008 1000 Genomes project Nature biotechnology 26 256 18327223
  34. [36]Hoen PA Ariyurek Y Thygesen HH Vreugdenhil E Vossen RH 2008 Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms Nucleic acids research 36 e141 18927111 PMC2588528
  35. [37]Wang ET Sandberg R Luo S Khrebtukova I Zhang L 2008 Alternative isoform regulation in human tissue transcriptomes Nature 456 470 476 18978772 PMC2593745
  36. [38]Wang Z Gerstein M Snyder M 2009 RNA-Seq: a revolutionary tool for transcriptomics Nature reviews 10 57 63 PMC2949280 19015660
  37. [39]Wheeler DL Barrett T Benson DA Bryant SH Canese K 2008 Database resources of the National Center for Biotechnology Information Nucleic acids research 36 D13 21 18045790 PMC2238880
  38. [40]Wilhelm BT Marguerat S Watt S Schubert F Wood V 2008 Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution Nature 453 1239 1243 18488015
  39. [41]Wu TD Watanabe CK 2005 GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics (Oxford, England) 21 1859 1875 15728110
  40. [42]Zhang Z Schwartz S Wagner L Miller W 2000 A greedy algorithm for aligning DNA sequences J Comput Biol 7 203 214 10890397

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Authors
Andrew F, N. A.
Venue
Journal of Computer Science & Systems Biology
Publisher
OMICS Publishing Group
Published
2008
Volume
01
Issue
01
Pages
132-132
ISSN
0974-7230 (ISSN-L)
DOI
10.4172/jcsb.1000013
PMC
PMC2819532
OpenAlex
W2078104861
Cited by
75
References
2
Citations by year
2024: 1 · 2022: 1 · 2021: 1 · 2020: 1 · 2019: 1 · 2018: 4 · 2017: 7 · 2016: 3 · 2015: 8 · 2014: 4 · 2013: 5 · 2012: 16
FWCI
3.16
Type
journal article
Language
en
Open access
Licence
other-oa
Locations
  • Journal of Computer Science & Systems Biology (publishedVersion, other-oa)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Nancy Davis Foundation for Multiple Sclerosis
  • Brigham and Women's Hospital
  • New Mexico State University
  • Genentech
  • National Institute of Allergy and Infectious Diseases
  • National Center for Research Resources (P20RR016480)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Keywords
Alpheus, next-generation sequencing, variant calling, single nucleotide polymorphisms, indels, splice variants, sequence abundance, transcriptome expression, differential gene expression, variant filtering, data visualization tools

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