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1
mkESA: enhanced suffix array construction tool.
Bioinformatics. 2009 Apr 15;25(8):1084-5. doi: 10.1093/bioinformatics/btp112. Epub 2009 Feb 26.
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gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections.
Algorithms Mol Biol. 2020 Sep 22;15:18. doi: 10.1186/s13015-020-00177-y. eCollection 2020.
3
A Simplified Description of Child Tables for Sequence Similarity Search.
IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2067-2073. doi: 10.1109/TCBB.2018.2796064. Epub 2018 Feb 9.
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Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array.
J Comput Biol. 2019 Sep;26(9):948-961. doi: 10.1089/cmb.2018.0230. Epub 2019 May 29.
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essaMEM: finding maximal exact matches using enhanced sparse suffix arrays.
Bioinformatics. 2013 Mar 15;29(6):802-4. doi: 10.1093/bioinformatics/btt042. Epub 2013 Jan 24.
7
Suffix tree searcher: exploration of common substrings in large DNA sequence sets.
BMC Res Notes. 2014 Jul 23;7:466. doi: 10.1186/1756-0500-7-466.
9
A bioinformatician's guide to the forefront of suffix array construction algorithms.
Brief Bioinform. 2014 Mar;15(2):138-54. doi: 10.1093/bib/bbt081. Epub 2014 Jan 10.
10
Reference-based genome compression using the longest matched substrings with parallelization consideration.
BMC Bioinformatics. 2023 Sep 30;24(1):369. doi: 10.1186/s12859-023-05500-z.

引用本文的文献

1
gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections.
Algorithms Mol Biol. 2020 Sep 22;15:18. doi: 10.1186/s13015-020-00177-y. eCollection 2020.
2
Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays.
Algorithms Mol Biol. 2016 Apr 23;11:9. doi: 10.1186/s13015-016-0068-6. eCollection 2016.
3
A bioinformatician's guide to the forefront of suffix array construction algorithms.
Brief Bioinform. 2014 Mar;15(2):138-54. doi: 10.1093/bib/bbt081. Epub 2014 Jan 10.
4
Querying large read collections in main memory: a versatile data structure.
BMC Bioinformatics. 2011 Jun 17;12:242. doi: 10.1186/1471-2105-12-242.
5
Geoseq: a tool for dissecting deep-sequencing datasets.
BMC Bioinformatics. 2010 Oct 12;11:506. doi: 10.1186/1471-2105-11-506.

本文引用的文献

1
Optimal spliced alignments of short sequence reads.
Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.
2
Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Bioinformatics. 2007 Apr 15;23(8):1026-8. doi: 10.1093/bioinformatics/btm039. Epub 2007 Feb 19.
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Fast index based algorithms and software for matching position specific scoring matrices.
BMC Bioinformatics. 2006 Aug 24;7:389. doi: 10.1186/1471-2105-7-389.
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Fast large scale oligonucleotide selection using the longest common factor approach.
J Bioinform Comput Biol. 2003 Jul;1(2):343-61. doi: 10.1142/s0219720003000125.
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Efficient multiple genome alignment.
Bioinformatics. 2002;18 Suppl 1:S312-20. doi: 10.1093/bioinformatics/18.suppl_1.s312.

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