HIV Molecular Immunology Database

Sequence histograms
The output page of the HIV sequence Search Interface offers a new option, "Make Histogram". This option shows the distribution of your sequences across the HIV genome. At each position across the graph, the number of sequences overlapping that position is plotted as a bar. Colors within the bars represent different subtypes. The histogram allows you to see at a glance what regions and what subtypes are represented in your output. 08 April 2009

Better names for downloaded sequences
The search interface now gives the option of customizing the names of downloaded sequences. After clicking the "download sequences" button on the search results, click the "compose a label" link and choose the database fields to make up the sequence labels. This makes it possible to save some or all of the search information in the sequence names. 07 April 2009

TreeRate
We have released TreeRate, a web tool for re-rooting trees. Trees can be re-rooted using several methods including algorithms that optimize roots using single or multiple longitudinal samples. The intention of re-rooting the trees is to find the most homogeneous ("clocklike") evolutionary rate in the tree. Our previous tool Branchlength is now part of the TreeRate tool. 11 March 2009

RSS Feeds
The HIV Databases now offer the option to subscribe to RSS feeds. These RSS feeds will consist of all updates that appear in our News. 11 March 2009

Special Interest Alignments
A new page provides HIV sequence alignments and accompanying data of special interest to research. Each set of data consists of one or more DNA sequence alignments, references, and any accompanying data that are available. Sets are selected for inclusion based on availability and the likelihood that researchers will have an interest in using the data in other studies. Your help is needed to suggest or provide additional sets of data for inclusion. 11 March 2009

PepMap
New tool PepMap is available. The tool maps an input set of peptides on the HXB2 reference sequence, generates a table with peptide locations and peptide protein maps, similar to epitope maps. 23 February 2009