Bioinformatics Tools

CompleteMOTIFs is a motif discovery platform developed to help biologists to find novel as well as known motifs in their peak datasets from transcription factor (TF) binding experiments such as ChIP-seq and ChIP-chip.

Lakshmi Kuttippurathu, Michael Hsing, Yongchao Liu, Bertil Schmidt, Douglas L. Maskell, Kyungjoon Lee, Aibin He, William T. Pu and Sek Won Kong. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics 2011 Mar 1;27(5):715-7.

MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq
Analysis pipeline for mapping mutations using RNA-seq without requiring parental strain information or a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. MMAPPR compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants.
Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Su YC, Yost HJ. MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq. Genome Research. 2013 Feb 4. [Epub ahead of print]

When supplied with a list of genes of interest in one species, OrthoRetriever delivers orthologs of those genes in other species.

Poly Peak Parser (beta) Targeted genomic mutagenesis techniques, including ZFN, TALEN and CRISPR-based approaches, have created a need to rapidly screen F1 animals for heterozygous short indels to identify germline mutation carriers and determine the nature of the mutation. Current techniques require PCR amplification of the genomic region surrounding the targeted site, subcloning into a plasmid vector, purification of plasmid DNA from multiple clones and Sanger sequencing runs on each clone to determine the genotype of a single animal. This process is tedious and inefficient when applied to the large number of individuals typically screened after targeted mutagenesis. Direct Sanger sequencing of a PCR amplified region surrounding the target site would be faster and more efficient, but the presence of an indel results in a string of “double peaks” due to the mismatched sequencing region beginning at and following the indel. Therefore, we have developed an online tool that separates ambiguous Sanger sequencing base calls into reference and alternative sequence, revealing the nature of the mutated sequence from a single sequencing run per individual without subcloning. Although designed for screening F1 animals after genome editing, this tool can also be used to identify indels in many contexts.

Founder Principle-Driven Enrichment Calculator Founder principle-driven enrichment (FPE) is a method that allows isolation of rare BAC recombinants (as rare as 1:10,000 to 1:100,000) without using selectable markers. The web-based calculator presented here enables users to easily determine all possible optimal FPE parameters for any desired cost function, i.e. the specific working conditions.

George T. Lyozin, Paul C. Bressloff, Amit Kumar, Yasuhiro Kosaka, Bradley L. Demarest, H. Joseph Yost, Michael R. Kuehn, and Luca Brunelli (Submitted). Isolation of rare recombinants without using selectable markers for one-step seamless BAC mutagenesis.