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#	Item
11	UGENE Quick Start Guide UGENE Quick Start Guide Quick Start Guide This document contains a quick introduction to UGENE. For more detailed information, you can find the UGENE User Manual and other Add to Reading List Source URL: ugene.unipro.ru Language: English - Date: 2013-10-09 09:26:00 MUSCLE Smith–Waterman algorithm Sequence alignment HMMER T-Coffee Multiple sequence alignment Sequence analysis UGENE BLAST Science Bioinformatics Computational phylogenetics
12	Lamprecht et al. Journal of Biomedical Semantics 2011, 2(Suppl 1):S5 http://www.jbiomedsem.com/content/2/S1/S5 RESEARCH JOURNAL OF Add to Reading List Source URL: www.jbiomedsem.com Language: English HMMER Ontology Semantic Web BioMOBY Sequence alignment Hidden Markov model EMBnet Workflow Soaplab Bioinformatics Science EMBOSS
13	Ensemble NMA across multiple species of DHFR Lars Skjaerven, Xin-Qiu Yao, Guido Scarabelli & Barry J. Grant October 1, 2014 This document provides Additional File 3 for Integrating protein structural dynamics and evoluti Add to Reading List Source URL: www.biomedcentral.com Language: English Gram-negative bacteria Gut flora Escherichia coli Pfam HMMER Bacteria Bioinformatics Enterobacteria
14	W h i t e P a p e r SGI High Throughput Computing (HTC) Wrapper Program for Bioinformatics Add to Reading List Source URL: www.sgi.com Language: English - Date: 2012-02-07 20:10:15 Computational science Parallel computing Silicon Graphics HMMER Altix High-throughput computing BLAST Sequence database Science Bioinformatics Computing
15	TRAVIS WHEELER CURRICULUM VITAE _________________________________________________________________________________ Department of Computer Science University of Montana Add to Reading List Source URL: www.cas.umt.edu Language: English - Date: 2014-08-02 14:09:26 Sequence alignment Multiple sequence alignment Computational biology Sean Eddy Computational genomics Sequence analysis HMMER Phylo Bioinformatics Science Computational science
16	MARSHALL PLAN SCHOLARSHIP PROGRAM REPORT Improvement of the scoring schemes in HMM protein anaylsis: e-values, p-values and alternatives to Viterby-scoring Add to Reading List Source URL: www.marshallplan.at Language: English - Date: 2014-09-30 21:01:26 Error detection and correction Statistics Dynamic programming Applied mathematics Computational science Hidden Markov model HMMER Viterbi algorithm Forward–backward algorithm Markov models Bioinformatics Science
17	MARSHALL PLAN REPORT Visual display of the 9-state profile hidden markov model prepared for the Austrian Marshall Plan Foundation in cooperation with Add to Reading List Source URL: www.marshallplan.at Language: English - Date: 2014-09-30 21:01:05 Applied mathematics Multiple sequence alignment Sequence alignment Hidden Markov model STING Protein family HMMER Phyre / Phyre2 Bioinformatics Science Biology
18	Austrian Marshall Plan Foundation Research Report Efficient estimation of p-values for HMModeller Supervisor: Add to Reading List Source URL: www.marshallplan.at Language: English - Date: 2014-09-30 21:01:14 Bioinformatics Normal distribution Mode Pareto distribution Viterbi algorithm Markov chain Hidden Markov model HMMER Statistics Markov models Probability and statistics
19	Why? Why are you learning this? “I’m [studying to be] a scientist, not a programmer. Why do I need to know how to program?” Add to Reading List Source URL: www.dalkescientific.com Language: English - Date: 2004-04-12 00:34:41 BioPerl Ensembl Biopython FASTA HMMER Bioinformatics Science BioJava
20	Protein Engineering vol.12 no.7 pp.527–534, 1999 Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologs V.Geetha1,2, Valentina Di Francesco3, Jean Garni Add to Reading List Source URL: mscl.cit.nih.gov Language: English Sequence alignment Threading Protein structure prediction BLAST Sequence motif HMMER Protein domain CASP Protein structure Bioinformatics Science Biology