/
references.txt
31 lines (25 loc) · 1.9 KB
/
references.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
References and Links
BLAST1: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
CD-HIT2: http://cd-hit.org/
CPC3: http://cpc.cbi.pku.edu.cn/
HMMER4: http://hmmer.org/
Infernal5: http://eddylab.org/infernal/
Pfam6: http://pfam.xfam.org/
Rfam7: http://rfam.xfam.org/
RSEM8: http://deweylab.github.io/RSEM/
SQLite: https://www.sqlite.org/
Trinity9: https://github.com/trinityrnaseq/trinityrnaseq/wiki
Trinotate: https://trinotate.github.io/
Vienna RNA Package10: https://www.tbi.univie.ac.at/RNA/
Uniprot-Sprot: http://www.uniprot.org/downloads
Uniprot-Uniref: http://www.uniprot.org/downloads
1. Camacho, C. et al. BLAST plus : architecture and applications. BMC Bioinformatics 10, - (2009).
2. Li, W. & Godzik, A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
3. Kong, L. et al. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, 345–349 (2007).
4. Eddy, S. R. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23, 205–211 (2009).
5. Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933–2935 (2013).
6. Bateman, A. The Pfam protein families database. Nucleic Acids Res. 32, 138D–141 (2004).
7. Nawrocki, E. P. et al. Rfam 12.0: Updates to the RNA families database. Nucleic Acids Res. 43, D130–D137 (2015).
8. Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
9. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–52 (2011).
10. Lorenz, R. et al. {ViennaRNA} Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).