Distributed Representations for Biological Sequence Analysis

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

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Computer analysis of protein sequences

Dayhoff, M · 1974

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Evolution of sequences within protein superfamilies

Dayhoff, M., McLaughlin, P., Barker, W., and Hunt, L · 1975

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Identification of common molecular subsequences

Smith, T. F., and Waterman, M. S · 1981

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Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J · 1990

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Amino acid substitution matrices from protein blocks

Henikoff, S., and Henikoff, J. G · 1992

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Predicting function: from genes to genomes and back

Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M., and Yuan, Y · 1998

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Scop: a structural classification of proteins database

Conte, L. L., Ailey, B., Hubbard, T. J., Brenner, S. E., Murzin, A. G., and Chothia, C · 2000

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Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

Huynen, M., Snel, B., Lathe, W., and Bork, P · 2000

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An efficient algorithm for large-scale detection of protein families

Enright, A. J., Van Dongen, S., and Ouzounis, C. A · 2002

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Multiple sequence alignment using clustalw and clustalx

Thompson, J. D., Gibson, T., Higgins, D. G., et al · 2002

Cited alongside, same era.

SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence

Cai, C. Z., Han, L. Y., Ji, Z. L., Chen, X., and Chen, Y. Z · 2003

Cited alongside, same era.

Mismatch string kernels for discriminative protein classification

Leslie, C. S., Eskin, E., Cohen, A., Weston, J., and Noble, W. S · 2004

Cited alongside, same era.

Distribution of words with a predefined range of mismatches to a dna probe in bacterial genomes

Melko, O. M., and Mushegian, A. R · 2004

Cited alongside, same era.

Hmmer-biosequence analysis using profile hidden markov models

Eddy, S., et al · 2007

Cited alongside, same era.

Sequencing technologies [mdash] the next generation

Efficient Estimation of Word Representations in Vector Space

Mikolov, T., Corrado, G., Chen, K., and Dean, J · 2013

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Distributed representations of words and phrases and their compositionality

Mikolov, T., Sutskever, I., Chen, K., Corrado, G. S., and Dean, J · 2013

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Uniprot: a hub for protein information

Consortium, U., et al · 2014

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Distributed representations of sentences and documents

Le, Q. V., and Mikolov, T · 2014

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Fast alignment-free sequence comparison using spaced-word frequencies

Leimeister, C.-A., Boden, M., Horwege, S., Lindner, S., and Morgenstern, B · 2014

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A new graphical representation of dna sequences using symmetrical vector assignment

Mizuta, S., and Yamaguchi, K · 2014