IgBLAST protocols

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IgBLAST specifications


Unique identifier OMICS_06083
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes



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Unique identifier OMICS_06083
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Roche
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Publication for IgBLAST

IgBLAST in pipeline

PMCID: 4658769
PMID: 26608341
DOI: 10.1186/s13073-015-0239-y

[…] by mapping the human genome, reads under 200 bp and reads with an average quality value of < q28. after quality filtering, immunediversity assigns ighv and ighj segment use to each read using igblast (http://www.ncbi.nlm.nih.gov/igblast/). incorrect assignment of the ighd segment is very common (approximately 50 % of the cases); therefore, the ighd assignment is omitted. for every […]

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IgBLAST in publications

PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z

[…] limitations, the possibility that some cells encoded iga instead of igg (we only selected for igm− cells), or false positive events in the flow cytometry. after sequencing pcr products, we used igblast (http://www.ncbi.nlm.nih.gov/igblast) and imgt® (http://www.imgt.org) to analyze igg gene usage and the extent of vh/vκ somatic hypermutation. we then cloned the pcr amplified variable […]

PMCID: 5928204
PMID: 29740455
DOI: 10.3389/fimmu.2018.00889

[…] an output of the translated amino acid protein sequence encoded by the open reading frame. we then aligned all of the protein sequences to the set of human germline ighv genes from imgt using igblast. based on the protein alignments and the imgt coordinate system, we then determined the framework and cdr regions of the full heavy chain variable region protein sequence. based on the cdr […]

PMCID: 5919685
PMID: 29659614
DOI: 10.1371/journal.ppat.1006967

[…] single cells analyzed in to sequence igλ variable regions from control (mock igλ+) and kshv-revised (igκ+ at infection, gfp+ igκ-igλ+ at 7dpi) lymphocytes and determined iglv gene usage using igblast. as expected[], control igλ clones were biased towards iglv gene families 1–3 with few clones utilizing iglv4-10. in contrast, kshv-modified igλ+ cells displayed increased usage of upstream […]

PMCID: 5882926
PMID: 29615812
DOI: 10.1038/s41598-018-23889-z

[…] the selection of positive transformants. selected colonies were picked and analyzed through sequencing by both vbase2 (http://www.vbase2.org/vbase2.php) and ncbi blast (http://www.ncbi.nlm.nih.gov/igblast/). sequences of the mabs were compared by clustal omega (http://www.ebi.ac.uk/tools/psa/emboss_needle/)., nucleotide sequences for the h and l chains of 6d2 and 8c3 were analyzed using […]

PMCID: 5879793
PMID: 29632541
DOI: 10.3389/fimmu.2018.00628

[…] we also included reads with partial barcode (minimum 4 bp) and the adjacent 4-bp primer sequence. in indexed library runs, reads with a minimum 8-bp primer sequence were also included.(2)initial igblast to identify bcr reads and join paired-ends: to remove non-bcr reads, we ran an initial in-house igblast using a germline database of only functional v-genes from imgt, rejecting reads […]

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IgBLAST institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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