mlgt (version 0.16)

mlgt-package: mlgt: Multi-locus geno-typing

Description

Package:

mlgt

Type:

Package

Version:

0.16

Date:

2012-03-27

Author:

Dave T. Gerrard

License:

GPL (>= 2)

LazyLoad:

yes

Details

mlgt sorts a batch of sequence by barcode and identity to templates. It makes use of external applications BLAST and MUSCLE. Genotypes are called and alleles can be compared to a reference list of sequences. More information about each function can be found in its help documentation.

Some text

The main functions are: prepareMlgtRun, mlgt, callGenotypes, createKnownAlleleList,

...

References

BLAST - Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman (1990). Basic local alignment search tool. Journal of molecular biology 215 (3), 403-410.

MUSCLE - Robert C. Edgar (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5), 1792-97.

IMGT/HLA database - Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SGE (2011) The IMGT/HLA Database. Nucleic Acids Research 39 Suppl 1:D1171-6