JOINSOLVER^® Sequence Submission Guidelines

JOINSOLVER^® requires the following sequence criteria for analysis:

1. The sequence must be from a human immunoglobulin variable region gene (heavy or light chain).
2. Heavy chain sequence alignments perform best when there are at least four out of five characters in the CTGGG motif from JH germline codons 102-104.
3. VH segment alignments perform best if codons: 83 to 94 (Kabat numbering), or 95 to 106 (IMGT numbering) are mostly intact.
4. For the most accurate analysis, the query sequence should not contain ambiguous nucleotides represented by 'X' or 'N'.

Acquiring JOINSOLVER^® sequence analysis:

1. From the JOINSOLVER^® menu select 'Enter Sequence'.
2. Type or paste your sequence name or accession number in the appropriate window(optional).
3. Type or Paste the sequence to query into the sequence window.
4. Depending on your choice of CDR boundary definitions or codon numbering, choose either Kabat/Chothia or IMGT.
5. According to whether your sequence is a heavy chain, kappa or lambda rearrangement, select the appropriate type of analysis.
6. By default, JOINSOLVER^® requires a minimum match length of 10, 5 and 5 nucleotides, for VH, (D) or JH segment alignment, respectively. However, you may enter a smaller number to decrease the stringency of sequence alignment or a larger number to increase it. Our analyses have determined that 8 to 12 consecutively matching base pairs are necessary to identify a D segment with 95% probability that it is not a random match. (For more details regarding D segment assignment, please select 'How JOINSOLVER^® Works' from the navigation bar.)
7. By default, JOINSOLVER^® displays a hierarchical list of the 5 VH, (D) or JH germline genes that most closely match the appropriate regions of the query sequence. However, you may enter a smaller or larger display number to view a lesser or greater number of matches. For example, if the first five matches for your query sequence are all allelic variants of one gene and you would like JOINSOLVER^® to display additional less closely related genes, JOINSOLVER^® will retrieve & display them if you enter a display number greater than 5.
8. The JOINSOLVER^® default mode provides automatic VHD and DJH junction analysis as well as mutation analysis. Deselecting either or both options removes the analysis from the results. If both options are deselected, JOINSOLVER^® will provide only VH(D)JH alignments.
9. Select the 'Submit Query' button and JOINSOLVER^® will provide your sequence analysis in a new window.

Print or save the JOINSOLVER^® sequence analysis from the JOINSOLVER^® Result page:

1. From your browser menu select 'FILE'.
2. To print, select 'PAGE SETUP', from 'ORIENTATION' select 'LANDSCAPE', then 'OK'. The landscape option is useful for printing sequences with longer than usual CDR3s. We suggest you use the landscape mode as your default printing set up. From the browser menu select 'FILE' then 'PRINT' or 'SAVE AS'.
3. Select 'PRINT' or 'SAVE'.