Development Process

We remove few nucleotide sequences with unusal frame shift in our database.

We add the Glycosylation information for each position in each gene, and we also provide the searching function for users.

We established web server to search cAb-Rep for similar antibodies, analysis of the prevalence of antibodies with specific genetic signatures, and estimation of reproducibility of somatic hypermutation patterns of interests.

Considering there are more high quality repertoires avaliable last year, we are extending our cAb-Rep database to incorpate these dataset. The first 2 datasets are:
a. Cinque Soto et. al,nature,2019
b. Bryan Briney et. al,nature,2019

We develop an script to search rare mutations in our GSSPs, we provide 2 different models:
a. Position model. In this model, users can search the mutability for 1 or more amino acid on a specifc Kabat position in V genes.
b. Sequence model. In this model, users can search rare mutations on all input sequences, the scripts will output mutability for each postion on a specific V gene.

We performed gene specific substitution profiles (GSSPs) analysis using our database, which generate 102 GSSPs.

We use Igdiscover10 to predict potential new germline genes in these donors, and then We re-annotate sequences in our database based on predictions. We also calculated the postion schemes (Kabat, IMGT and Chothia) by ANARCI and provide new postion model in Ab_search.py to search similar reads in our database.

We build a new pipline based on SONAR to handle those Raw data from different sources. Briefly we remove low quality samples and sequences which did not pass our criteria. Then SONAR pipline were employed to annotate all sequences in our database, the sequence annotation information in our database include:
a. Sample name, Project name, Donor ID
b. Healthy and Disease information
c. V gene, J gene, C gene
d. CDR3 nucleotide, CDR3 amnino acid, CDR3 length
e. Additional information

In this version of cAb-Rep database, we would like to search similar signature sequences from our collected sequences, we create Ab_search.py to search antibody sequences use CDR3 model

In late 2017, we were collecting high qualty sequencing data for human B cell repertoires, with the criteria for high quality:
a. 2x250 or 2x300 Miseq
b. Illumina platform
c. More than 2000 Unique reads
d. Typical Miseq sequencing quality
e. 5'RACE or Gene specific primer amplification