Main Page

From kmer
Jump to: navigation, search

The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers.



High-throughput cDNA to whole genome alignments using a powerful k-mer based filter coupled with sim4db.


A2Amapper, ATAC, Assembly To Assembly Comparison

Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).


Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.


sim4db files

The output of snapper, ESTmapper and sim4db is in the sim4db format. We provide many utilities for processing this format, including converting to GFF3.


LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.


An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.