HMMvar & HMMvar-func

Please download the latest version from here. Other release information is available at Github.

Release notes (Major updates):

HMMvar-func is available at here.

Pre-computed scores for variants from 1000 Genomes project

Based on the 1000 Genomes Project variants (Phase I), the compensatory mutations (CM) sets and non-compensatory mutations (nonCM) sets are available for you to download. All the compound homozygous set scores and single variants scores are also provided. To know the details about these sets, please read the paper. (table schema)

CM set scores: there is probably a compensatory effect by combining the variants in the set.

nonCM set scores: the effects of single variants are reserved in the set.

Set scores: all the compound homozygous mutations determined by the genotypes and ancestral alleles are scored.

Single scores: single variants in the above sets are also scored.

Pre-computed functional outcome for disease/cancer variants

Some pre-computed types of mutations in disease/cancer related genes can be found at here. It includes the confidence scores and predicted types of mutations in thyrotropin receptor (TSHr, Table 1), tumor suppressor protein 53 (TP53, Table 2), epidermal growth factor receptor (EGFR, Table3), and B-Raf proto-oncogene, serine/threonine kinase (BRAF, Table 4).

Pre-computed profile hidden Markov models

22,004 precomputed profile HMMs are gethered for you to play with your own variants data sets. These HMMs are generated by HMMER3 tool based on the multiple alignments of 45 vertebrate genomes with Human obtained from UCSC database. Each file is an HMM corresponding to a specific protein sequence (the file name indicates the reference transcript).Please find the HMMs here(1.05G).

We recommend to use a downloading manager or tool (e.g. wget) that allow you to continue interupted downloads due to the big size of the files.