iHMMune-align web-based access

A HMM-based Partitioning Utility for the Human Immunoglobulin Heavy Chain

Partitioning Sequences:

Input sequences may be provided as pasted text into the text area provided or as a file in FASTA format. iHMMune-align can be executed with default parameters simply by clicking the 'Run iHMMune-align' button after providing input data. Please see the here for more detail on setting of advanced parameters.

Please note that upon output of the results all files are removed from the server.

Reference:

Gaeta BA, Malming HR, Jackson KJ, Bain ME, Wilson P, Collins AM (2007) iHMMune-align: Hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics 23:1580-1587


Paste a sequence or select an input file: The sequence(s) must be in FASTA format. Note: the radio button next to the selected source of input must be checked. Use the 'Range' option below if output is only required for a subset of sequences in a file. If output is not required for all input sequences then indicate the range for which output should be provided.	Paste a FASTA sequence into the box below: Use the 'Browse...' button to locate a file in FASTA format: Start at sequence and finish at
No. of IGHV results to return: Set the number of alternative IGHV results to be returned for each input sequence. The HMM partitioning results for the prescribed number of germline IGHV genes will be returned. Note: each additional IGHV result creates another instance of the HMM and therefore increases the processing time for each sequence.	Top germline IGHV results to be displayed
Output format: Specify the format in which results should be output. The most complete of the outputs is CSV. The other outputs are suitable for display on the webpage and each give different data. Please see here for a description and examples of each of the output formats.	CSV Output HTML Summary Display alignment and mutation details: Yes No
Germline repertoires: These are the sets of germline IGHV, IGHD and IGHJ to which are used for determination of the V-REGION, D-REGION and J-REGION. Custom reprtoires must be in FASTA format and must include IGHV/IGHD/IGHJ as part of the sequence identification line.	IGHV iHMMune-align expressed IGHV repertoire Combined IHMMune-align, IMGT and VBASE2 repertoire Custom IGHD Expressed IGHD Repertoire Custom IGHJ Expressed IGHJ Repertoire Custom
Minimum IGHD Length: Specifies the minimum length of the D-REGION to be identified. Selecting dynamic will allow the minimum IGHD length to be calculated based on the IGHD length and number of mutations in the context of the junction. Alternatively, minimum D-REGION lengths can be specified. If using this option it is recommended that a minimum of 8 nucleotides be used, however, the option for shorter D-REGIONs (5nts) is provided.	Dynamic - probability based Five nucleotides Eight nucletides
Mutability Scoring Based on: Specify if mutability scores are to be calculated using mutation potential based on trinucleotides or if calculations should be based on presence or absence of hotspots.	Hotspots Trinucleotides
Model Probabilities: Probabilities for N-addition and exonuclease removal can be adjusted through the use of a custom file. Probabilities of N-addiiton or specified separately for the N1 and N2 regions and each IGHV/D/J gene family have their own exonuclease probabilities. Please see here for details of probability file format.	Default Exonuclease and N addition Probabilities Custom Probabilities from file
Scoring Matrix (for IGHV alignment): The SmithWaterman Algorithm is used for the identification of the putative IGHV gene. The nucleotide scoring matrix that is used for this alignment can be specified here. A custom scoring matrix can be used. Please see here for the required format of a custom matrix. *Note: The scoring matrix selected does* influence that outcome of the partitioning process. Please select carefully.**	Scoring Matrix: If using a custom matrix please select the file location: