Welcome to biowiki.org, an online notebook for Ian Holmes' research group at the University of California, Berkeley.
- 1 About
- 2 Software
- 2.1 Genome informatics
- 2.2 Molecular evolution
- 2.3 Other bioinformatics tools
- 2.4 Non-bioinformatics tools
- 3 Writing
Information about the group.
- Holmes lab members
- PhD: Jordi Silvestre Ryan
- Programmer: Eric Yao
- PI: Ian Holmes
- Address: 381 Stanley Hall, University of California, Berkeley, CA 94720-3220.
- Phone: (510) 666 - 2791.
Links to software developed by the group.
- Buels et al.: JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66.
Apollo, the online curation platform, is built on top of JBrowse:
- Lee et al.: Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013;14:R93.
Biomake is a port of GNU Make that allows MD5 signatures, job submission to queues, multiple wildcards per rule, and logic programming extensions.
- Holmes IH & Mungall CJ. 2016. BioMake: a GNU Make-compatible utility for declarative workflow management.
Historian is a program for ancestral sequence reconstruction, using phylogenetic Markov chain models of substitutions and indels. In our tests (as of 2016) it's the most accurate tool for reconstructing ancient sequences and rates.
xrate is software for fitting structured phylogenetic models to multiple sequence alignments. It's been used to estimate many substitution models, including these ones:
- Le & Gascuel: An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008;25:1307-20.
- Kosiol et al.: An empirical codon model for protein sequence evolution. Mol. Biol. Evol. 2007;24:1464-79.
- De Maio et al.: Estimating empirical codon hidden Markov models. Mol. Biol. Evol. 2013;30:725-36.
It can also be used to fit structured phylogenetic grammars to multiple alignments, e.g. as described here:
- Westesson & Holmes: Developing and applying heterogeneous phylogenetic models with XRate. PLoS ONE 2012;7:e36898.
- Bradley et al.: Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS ONE 2009;4:e6478.
And it can do ancestral sequence reconstruction:
- Santiago-Ortiz et al.: AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Ther. 2015;22:934-46.
Some more links:
- Tutorial on using xrate
- Background on phylogenetic grammars
- xrate format - documentation of the xrate model format
stemloc is software for simultaneous alignment and folding of RNA.
- Holmes &: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 2005;6:73.
- Bradley et al.: Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics 2008;24:2677-83.
Other bioinformatics tools
The lab provides several tools for manipulating standard bioinformatics file formats:
- Stockholm Tools for working with the Stockholm format
- Gff Tools for working with the GFF format
dnastore is software for encoding and decoding information in DNA sequences using error-tolerant codes that are robust to insertions, deletions and duplications
- Holmes, 2016. Modular non-repeating codes for DNA storage
wtfgenes is software implementing the MCMC method of Bauer _et al_ for gene set analysis using the Gene Ontology
- Bauer et al.: GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res. 2010;38:3523-32.
quaff is a Pair HMM for aligning Oxford nanopore reads.
Boswell is an experimental IDE for authoring and hosting multi-player choice-based interactive fiction.
- Source code
- Holmes, 2014. A Web-Based Editor for Multiplayer Choice Games. Proceedings of the 9th International Conference on the Foundations of Digital Games.
This wiki was hosted for many years using TWiki. For various mundane reasons we eventually moved it to Mediawiki. To do this we modified a script originally written by Ryan Castillo. Our updated version of this script is linked below.
Random rants on this wiki.
Essays on algorithms and applications
- String Transducers: finite state machines for molecular evolution
- Stochastic Grammars
- Phylogenetic Alignment
Collections of links to papers
- Transposon Papers: bioinformatic annotation of transposons
- Phylogenetic Alignment Reader: multiple alignment with evolutionary models
- Nucleic Acid Engineering: synthetic DNA & RNA machines