Ab-origin statistics

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chevron_left V(D)J assignment Immunoglobulin rearrangement detection chevron_right
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Ab-origin specifications

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Unique identifier OMICS_20613
Name Ab-origin
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability No
Maintained No

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Publication for Ab-origin

Ab-origin in publications

 (5)
PMCID: 5888833
PMID: 29637082
DOI: 10.1177/2325967118762751

[…] directly onto the soft tissue of the ab)., the distances between the centers of these footprints to key bony and chondral structures are outlined in . most notably, the perceived center of the ab origin was located 11.7 ± 1.4 mm from the medial epicondyle, 13.9 ± 1.7 mm from the trochlear margin, and 5.4 ± 0.9 mm from the center of the pb insertion. the apparent center of the ab insertion […]

PMCID: 4528417
PMID: 26194754
DOI: 10.1098/rstb.2014.0240

[…] v, d and j genes must be identified and assigned to their respective germline genes. methods for v(d)j assignment fall into two classes: alignment-based methods (joinsolver [], imgt/v-quest [,], ab-origin [] and igblast []), and model-based methods (e.g. ihmmunealign [], soda [], and soda2 [] which are based on hidden markov models, and others [,]). however, none of these approaches take […]

PMCID: 4177983
PMID: 25254371
DOI: 10.1371/journal.ppat.1004403

[…] developing unconventional vaccination strategies to target exceptional abs in the long term., the 4e10 heavy and light chain nucleotide sequences were analyzed using joinsolver , imgt/v-quest , , ab-origin , soda and ihmmune to compositely identify segments with the fewest nucleotide mismatches, generating a combinatorial ensemble of 12 geps (). each derived gep candidate consisted […]

PMCID: 3764224
PMID: 24039582
DOI: 10.1371/journal.ppat.1003619

[…] vector to yield vector ptol2pifnl1mc-f. the fragment includes exon 1 including the first codons of the zebrafish ifnφ1 orf. this construct was co-injected with tol2 mrna into 1-cell stage eggs of ab origin ., injections and handling of larvae were performed as described . briefly, zebrafish larvae aged 70–72 hpf were inoculated by microfinjection of ∼102 tcid50 chikv (∼1 nl of supernatant […]

PMCID: 2946782
PMID: 20875155
DOI: 10.1186/1745-7580-6-S1-S4

[…] studies have demonstrated the importance and potential of accurate alignment and analysis for studying the immune response, using software such as imgt/v-quest [] , soda [], ihmmune-align [], ab-origin [], etc. however, none of these programs allow the direct identification of clonally-related immunoglobulin gene sets., the third complementarity determining region (cdr3) is a highly […]


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Ab-origin institution(s)
Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China; College of Life science and Biotechnology, Tongji University, Shanghai, China
Ab-origin funding source(s)
Supported in part by grants from Ministry of Science and Technology China (2004CB720103, 2006AA02Z317), National Natural Science Foundation of China (30500107), Shanghai Municipal Education Commission (2000236018, 2000236016) and Science and technology commission of Shanghai municipality (06PJ14072).

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