"Why can't I find human VH3-23 sequences?"
Unfortunately, there are many different gene naming formats, and iReceptor can't search over all of them. We have chosen to use the widely accepted IMGT Nomenclature. This means you can search for "IGHV3-23" under the V-Gene Allele filter on the Sequence Search page. This search does have to begin with "IGH", but you can widen your results by including less of the gene, e.g. by writing only "IGHV3".
"What's the difference between Bookmark this search and Download these sequences?"
Bookmarking a search is a in-browser action that just saves the parameters of the search that you did. Downloading sequences saves the actual results of the parameters of your search to your computer's hard drive.
"Why are some individual metadata columns empty?"
Unfortunately, some columns in our metadata are not always complete. This could be for one of a couple reasons:
- Data was not reported. Much of our data comes from public papers that are then curated by our in-house Data Curator. Any subject or sample metadata column could be left empty due to lack of information from a paper itself. Ex. Race often has no entries; this data was likely not provided by the authors.
- Data is not available. If data appears to be missing from an external repository, this could either be, again, because authors did not collect it (ex. subject information), or that they did not store the data on their end, but we asked for it on ours. As we follow the MiAIRR standards, we capture a lot of information that other sources do not always fully follow. As AIRR compliance evolves and becomes more widespread, this should become less of a problem.
Of course, if genes or V, and J calls are absent, there is the possibility of a further issue with the data-set (files not correctly uploaded, etc.), and errors of that nature should be brought to our attention.