Hepatitis C Virus Databases

The Hepatitis C Virus (HCV) Database Project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The HCV database group strives to present HCV-associated genetic and immunologic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools. We are assisted in this effort by an editorial board, whose members serve as 'representatives' of the user community and keep us apprised of problems and issues that we might otherwise miss.

This project is deeply indebted to the HIV Database Group, led by Dr. Bette Korber, for much of its tools, infrastructure and philosophy; the two databases continue to collaborate closely and to share software and resources.

News

The Codon alignment tool can restore codons in your alignment so that the resulting alignment can be immediately translated. Currently this tool requires an input reading frame (or does its work for all 3 frames). In the future we will connect it to the reference sequence and the 'locate' tool so that it can find the correct reading frame automatically. 21 June 2008

There are new ready-made alignments for all categories (all, consensus, and genotype reference). They are called '2008 alignments' and are now the default for the alignment interface. 26 May 2008

We added a beta version of the new tool HCValign, which uses our HCV HMM alignment model to align user sequences. It can also codon-align the sequences, and separate individual HCV genes, and thus is a near-successor to Gene cutter. Please note that the tool has not yet been extensively tested. We would appreciate bug reports and other feedback. 07 May 2008

Citing these databases:

HCV sequence database: Kuiken C, Yusim K, Boykin L, Richardson R. The Los Alamos HCV Sequence Database. Bioinformatics(2005), 21(3):379-84.

HCV immunology database: Yusim K, Richardson R, Tao N, Szinger J, Funkhouser R, Korber B, Kuiken C. The Los Alamos Hepatitis C Immunology Database. Applied Bioinformatics 2005;4(4).

Questions or comments? Contact us at hcv-info@lanl.gov