The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database is an integrated resource storing sequences of annotated immunoglobulin variable domains (Igs) obtained from the NCBI database (22) and enriched with tools for searching and analyzing them.
The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementary determining regions, assignment of their structural class and identification of mutations with respect to the germline are computed on the fly and can also be retrieved for user submitted sequences.
This release contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type)
The user can directly query the database by antigen type, canonical structure, germline family or run customized Blast searches. Automatic building of three-dimensional models of the domains can be performed using the PIGS web server (14).
Only retrieves Igs for which the correctly paired light and heavy chain sequences are available.
DBsearch output page
Lists the entries matching the query. By clicking the Analyze button (labelled with "A") the DBsearch tool is launched using the selected chain as query (see later).
The NCBI Id is linked to a Feature page for the Ig described later, the Definition to the NCBI entry, the Reference to the related PubMed record.
The list can be sorted according to the content of each column by clicking on its header. Columns can be moved around using the mouse.
Allows the input (manually or by uploading a file) of either an amino acid or a nucleotide sequence (one-letter code, fasta or raw format) of the light and/or heavy chain and performs the appropriate Blast search on the database entries.
Sequence Search output page
The system performs one or more Blast searches with default parameters. If the input consists of a light and heavy chain the database is searched with the light chain, with the heavy chain and with both.
By clicking the Analyze button (labelled with "A") a new seqrch is launched using the selected chain as query (see later).
New tabs appear after a search or upon requesting an analysis of the sequence:
BlastL, BlastH and BlastL+H
The first tab(s) (BlastL, BlastH and/or BlastL+H) provide the Blast results for the light and heavy chain and those obtained by concatenating the two chains and searching a dataset where paired light and heavy chain sequences are concatenated as well.
They display a table the first 250 sequences (according to the E-value) found by Blast in the appropriate set of sequences. The first five columns are as in the DBsearch output page. Additional columns contain the % sequence identity and the E-value. Also in this case, the list can be sorted according to the content of each column by clicking on its header. Columns can be moved around using the mouse
Reports the alignment of the input sequence with the commonly used Kabat-Chothia numbering scheme (20).
The canonical structures (describing the main chain conformation of the Complementary Determining Regions) are reported together with the length of the CDRs.
This is a summary reporting the sequences of the various regions of the molecule separately in the order they appear in the sequence (Framework 1, CDR1, Framework 2, CDR2, Framework 3, CDR3 and Framework 4).
Includes information about the mutations with respect to the germline of the selected sequence. According to whether the input sequence was provided as a nucleotide or amino acid sequence, nucleotide or amino acid variations are shown. The Blosum62 score is also shown below each mutation. This information is obtained by blasting the sequences on a dataset of over 2.000 genes from human, mouse (for which the complete germline repertoire is available) and several other species. .
It launches the PIGS immunoglobulin modeling tool (14) to build a 3D model of the input sequence through. This tool is available only if both VL and VH sequences were submitted.
It is possible to browse the db by selecting the chain type and (optionally) the progressive number of the entry from which starting to browse.
The browse output page contains a list of 25 entries and two buttons to move to the next or to the previous 25 entries.
One or more of the following buttons are on result tables
Saves the page in one of the following formats: Text only, Excel, CSV, PDF
Displays a printer-friendly version of the page. Use Esc or the button at the top of the page to go back to the previous page
Opens a new window displaying the alignment of all and only the Igs visible on the page.In case of paired Igs, the alignment will display heavy and light chain sequences on the same line divided by the '//' symbol.
Amino acids or nucleotides different from those of the selected (or first) sequence are highlighted in red
This box is situated on the top right corner of the table. Samples that do not contain the text inserted the filter box are temporarily hidden.
The number of Igs to be shown in the current table.
Results can be sorted according to all the columns displaying the icon. All the columns can be moved by clicking and dragging them in the new position.
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