The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Infernal 1.1: 100-fold faster RNA homology searches
Open accessAbstract
Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches. Availability: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user’s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. Contact: nawrockie@janelia.hhmi.org
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
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Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab688 · Cited by 1,925
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
Chan, P. P., & Lowe, T. M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1309 · Cited by 1,051
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Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B., Hu, Z., Chen, S., Pental, D., Ju, Y., et al. (2016) · Nature Genetics · doi:10.1038/ng.3657 · Cited by 580
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Forster, S. C., Kumar, N., Anonye, B. O., Almeida, A., Viciani, E., Stares, M. D., Dunn, M., Mkandawire, T. T., Zhu, A., Shao, Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0009-7 · Cited by 580
Metadata
- Authors
- Nawrocki, E. P., & Eddy, S. R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-09-04
- Volume
- 29
- Issue
- 22
- Pages
- 2933-2935
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2141152740
- Cited by
- 3,591
- References
- 2
- FWCI
- 30.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
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