메뉴 건너뛰기




Volumn 30, Issue 17, 2014, Pages

Lambda: The local aligner for massive biological data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; PROCEDURES; SEQUENCE ALIGNMENT;

EID: 84907028625     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu439     Document Type: Conference Paper
Times cited : (55)

References (42)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S. et al. (1990) Basic local alignment search tool. J.Mol. Bio., 215, 403-410.
    • (1990) J.Mol. Bio , vol.215 , pp. 403-410
    • Altschul, S.1
  • 2
    • 0029889221 scopus 로고    scopus 로고
    • Local alignment statistics
    • Altschul, S.F. and Gish, W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
    • (1996) Methods Enzymol , vol.266 , pp. 460-480
    • Altschul, S.F.1    Gish, W.2
  • 3
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 4
    • 27144489108 scopus 로고    scopus 로고
    • Protein database searches using compositionally adjusted substitution matrices
    • Altschul, S.F. et al. (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J., 272, 5101-5109.
    • (2005) FEBS J , vol.272 , pp. 5101-5109
    • Altschul, S.F.1
  • 5
    • 61449164029 scopus 로고    scopus 로고
    • Automated alphabet reduction for protein datasets
    • Bacardit, J. et al. (2009) Automated alphabet reduction for protein datasets. BMC Bioinformatics, 10, 6.
    • (2009) BMC Bioinformatics , vol.10 , pp. 6
    • Bacardit, J.1
  • 6
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • Bazinet, A.L. and Cummings, M.P. (2012) A comparative evaluation of sequence classification programs. BMC Bioinformatics, 13, 92.
    • (2012) BMC Bioinformatics , vol.13 , pp. 92
    • Bazinet, A.L.1    Cummings, M.P.2
  • 7
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho, C. et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 8
    • 0026693729 scopus 로고
    • Aligning two sequences within a specified diagonal band
    • Chao, K.M. et al. (1992) Aligning two sequences within a specified diagonal band. CABIOS, 8, 481-487.
    • (1992) CABIOS , vol.8 , pp. 481-487
    • Chao, K.M.1
  • 9
    • 0002806690 scopus 로고    scopus 로고
    • Openmp: An industry-standard api for shared-memory programming
    • Dagum, L. and Menon, R. (1998) OpenMP: An Industry-Standard API for Shared-Memory Programming. IEEE Comput. Sci. Eng., 5, 46-55.
    • (1998) IEEE Comput. Sci. Eng , vol.5 , pp. 46-55
    • Dagum, L.1    Menon, R.2
  • 10
    • 39549090389 scopus 로고    scopus 로고
    • SeqAn An efficient, generic C++ library for sequence analysis
    • Döring, A. et al. (2008) SeqAn An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9, 11.
    • (2008) BMC Bioinformatics , vol.9 , pp. 11
    • Döring, A.1
  • 11
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 12
    • 84875690380 scopus 로고    scopus 로고
    • Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms
    • Eikmeyer, F.G. et al. (2013) Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Biotechnol. Biofuels, 6, 49.
    • (2013) Biotechnol. Biofuels , vol.6 , pp. 49
    • Eikmeyer, F.G.1
  • 13
    • 75249093378 scopus 로고    scopus 로고
    • MicroRazerS: Rapid alignment of small RNA reads
    • Emde, A.K. et al. (2010) MicroRazerS: rapid alignment of small RNA reads. Bioinformatics, 26, 123-124.
    • (2010) Bioinformatics , vol.26 , pp. 123-124
    • Emde, A.K.1
  • 14
    • 80051735813 scopus 로고    scopus 로고
    • Taxonomic classification of metagenomic shotgun sequences with CARMA3
    • Gerlach, W. and Stoye, J. (2011) Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res., 39, e91.
    • (2011) Nucleic Acids Res , vol.39
    • Gerlach, W.1    Stoye, J.2
  • 15
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh, O. (1981) An Improved Algorithm for Matching Biological Sequences. J. Mol. Bio., 162, 705-708.
    • (1981) J. Mol. Bio , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 16
    • 0016518550 scopus 로고
    • A linear space algorithm for computing maximal common subsequences
    • Hirschberg, D.S. (1975) A linear space algorithm for computing maximal common subsequences. Commun. ACM, 18, 341-343.
    • (1975) Commun ACM , vol.18 , pp. 341-343
    • Hirschberg, D.S.1
  • 17
    • 84891349082 scopus 로고    scopus 로고
    • A poor mans blastx-high-throughput metagenomic protein database search using pauda
    • Huson, D.H. and Xie, C. (2013) A poor mans blastx-high-throughput metagenomic protein database search using pauda. Bioinformatics, 30, 38-39.
    • (2013) Bioinformatics , vol.30 , pp. 38-39
    • Huson, D.H.1    Xie, C.2
  • 18
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • Huson, D.H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
    • (2007) Genome Res , vol.17 , pp. 377-386
    • Huson, D.H.1
  • 19
    • 80053483140 scopus 로고    scopus 로고
    • STELLAR: Fast and exact local alignments
    • Kehr, B. et al. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (Suppl. 9), S15.
    • (2011) BMC Bioinformatics , vol.12 SUPPL. 9
    • Kehr, B.1
  • 20
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The BLAST-like alignment tool
    • Kent, W.J. (2002) BLAT-The BLAST-like alignment tool. Genome Res., 12, 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 21
    • 84866458775 scopus 로고    scopus 로고
    • SANS: High-throughput retrieval of protein sequences allowing 50% mismatches
    • Koskinen, P. and Holm, L. (2012) SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics, 28, 438-443.
    • (2012) Bioinformatics , vol.28 , pp. 438-443
    • Koskinen, P.1    Holm, L.2
  • 22
    • 42449162998 scopus 로고    scopus 로고
    • Phylogenetic classification of short environmental DNA fragments
    • Krause, L. et al. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res., 36, 2230-2239.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2230-2239
    • Krause, L.1
  • 23
    • 79955794476 scopus 로고    scopus 로고
    • Comparative fecal metagenomics unveils unique functional capacity of the swine gut
    • Lamendella, R. et al. (2011) Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol., 11, 103.
    • (2011) BMC Microbiol , vol.11 , pp. 103
    • Lamendella, R.1
  • 24
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 25
    • 0038451355 scopus 로고    scopus 로고
    • Reduction of protein sequence complexity by residue grouping
    • Li, T. et al. (2003) Reduction of protein sequence complexity by residue grouping. Protein Eng., 16, 323-330.
    • (2003) Protein Eng , vol.16 , pp. 323-330
    • Li, T.1
  • 26
    • 84892491111 scopus 로고    scopus 로고
    • Comparison of next-generation sequencing systems
    • Liu, L. et al. (2012) Comparison of next-generation sequencing systems. J. Biomed. Biotechnol., 2012, 11.
    • (2012) J. Biomed. Biotechnol , vol.2012 , pp. 11
    • Liu, L.1
  • 27
    • 83555174830 scopus 로고    scopus 로고
    • Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
    • Mackelprang, R. et al. (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature, 480, 368-371.
    • (2011) Nature , vol.480 , pp. 368-371
    • Mackelprang, R.1
  • 28
    • 0001338954 scopus 로고    scopus 로고
    • Simplified amino acid alphabets for protein fold recognition and implications for folding
    • Murphy, L.R. et al. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng., 13, 149-152.
    • (2000) Protein Eng , vol.13 , pp. 149-152
    • Murphy, L.R.1
  • 29
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Bio., 48, 443-453.
    • (1970) J. Mol. Bio , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 30
    • 0023812695 scopus 로고
    • Characterization of a helical protein designed from first principles
    • Regan, L. and DeGrado, W.F. (1988) Characterization of a helical protein designed from first principles. Science, 241, 976-978.
    • (1988) Science , vol.241 , pp. 976-978
    • Regan, L.1    Degrado, W.F.2
  • 31
    • 0018524481 scopus 로고
    • Degeneracy of the information contained in amino acid sequences: Evidence from overlaid genes
    • Sander, C. and Schul, G. (1979) Degeneracy of the information contained in amino acid sequences: evidence from overlaid genes. J. Mol. Evol., 13, 245-252.
    • (1979) J. Mol. Evol , vol.13 , pp. 245-252
    • Sander, C.1    Schul, G.2
  • 32
    • 84876548372 scopus 로고    scopus 로고
    • Fast and accurate read mapping with approximate seeds and multiple backtracking
    • Siragusa, E. et al. (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res., 41, e78.
    • (2013) Nucleic Acids Res , vol.41
    • Siragusa, E.1
  • 33
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T. and Waterman, M. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol , vol.147 , pp. 195-197
    • Smith, T.1    Waterman, M.2
  • 34
    • 84878276414 scopus 로고    scopus 로고
    • Life in the dark: Metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism
    • Tetu, S.G. et al. (2013) Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism. ISME J., 7, 1227-1236.
    • (2013) ISME J , vol.7 , pp. 1227-1236
    • Tetu, S.G.1
  • 35
    • 85026758927 scopus 로고
    • Approximate string-matching over suffix trees
    • Apostolico, A. et al. eds Springer, Berlin/Heidelberg/New York
    • Ukkonen, E. (1993) Approximate string-matching over suffix trees. In: Apostolico, A. et al. (eds) Combinatorial Pattern Matching, Vol. 684 of Lecture Notes in Computer Science. Springer, Berlin/Heidelberg/New York, pp. 228-242.
    • (1993) Combinatorial Pattern Matching of Lecture Notes in Computer Science , vol.684 , pp. 228-242
    • Ukkonen, E.1
  • 36
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the sargasso sea
    • Venter, J.C. et al. (2004) Environmental genome shotgun sequencing of the sargasso sea. Science, 304, 66-74.
    • (2004) Science , vol.304 , pp. 66-74
    • Venter, J.C.1
  • 37
    • 69749106334 scopus 로고    scopus 로고
    • RazerS-fast read mapping with sensitivity control
    • Weese, D. et al. (2009) RazerS-fast read mapping with sensitivity control. Genome Res., 19, 1646-1654.
    • (2009) Genome Res , vol.19 , pp. 1646-1654
    • Weese, D.1
  • 38
    • 84870471176 scopus 로고    scopus 로고
    • RazerS 3: Faster, fully sensitive read mapping
    • Weese, D. et al. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28, 2592-2599.
    • (2012) Bioinformatics , vol.28 , pp. 2592-2599
    • Weese, D.1
  • 39
    • 40549141418 scopus 로고    scopus 로고
    • Metagenomics: Read length matters
    • Wommack, K.E. et al. (2008) Metagenomics: read length matters. Appl. Environ. Microbiol., 74, 1453-1463.
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 1453-1463
    • Wommack, K.E.1
  • 40
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton, J.C. and Federhen, S. (1993) Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases. Comput. Chem., 17, 149-163.
    • (1993) Comput. Chem , vol.17 , pp. 149-163
    • Wootton, J.C.1    Federhen, S.2
  • 41
    • 79955877212 scopus 로고    scopus 로고
    • RAPSearch: A fast protein similarity search tool for short reads
    • Ye, Y. et al. (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics, 12, 159.
    • (2011) BMC Bioinformatics , vol.12 , pp. 159
    • Ye, Y.1
  • 42
    • 84855167751 scopus 로고    scopus 로고
    • RAPSearch2: A fast and memory-efficient protein similarity search tool for next-generation sequencing data
    • Zhao, Y. et al. (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics, 28, 125-126
    • (2012) Bioinformatics , vol.28 , pp. 125-126
    • Zhao, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.