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.
- Getting Started with ESTmapper
- ESTmapper Documentation (Much nicer PDF version.)
- A poster presented at GSAC 2005.
High-throughput searching and alignment of short to medium length genomic DNA to a genome.
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.
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.
- Sim4db revision 1895 was released on 20 Jan 2011.
- Sim4db revision 1896 was released on 21 Mar 2011. This version fixes a failure when
The two sequences are not really similar.
(1 1000; 53391 90 53390 89)
Please try exact phase 1 method
- There are no releases of the entire project or other tools, use Subversion to download the code instead.