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Protocols

Jalview specifications

Information


Unique identifier OMICS_00885
Name Jalview
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Jalview

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Maintainer


  • person_outline Geoffrey J. Barton

Publications for Jalview

Jalview citations

 (1020)
library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] ch against NCBI Non-redundant protein set on ANNOTATOR [] and were used to create a multiple sequence alignment with MAFFT (L-INS-I settings) []. We deleted those sequences that have large gaps using Jalview [].A SNP is located in the functional domain of a protein. We used the amino acid sequence of the gene that the SNP is located in as input to do “Prim-Seq-An w/Pfam” analysis in ANNOTATOR [] u […]

library_books

Detection of Chlamydiaceae and Chlamydia like organisms on the ocular surface of children and adults from a trachoma endemic region

2018
Sci Rep
PMCID: 5943520
PMID: 29743637
DOI: 10.1038/s41598-018-23887-1

[…] 7.1), Criblamydia sequanensis strain CRIB-18 (NR_115696.1), S. negevensis strain Z (NR_029194.1), and P. acanthamoebae strain CRIB43 (FJ532291.1) were used. Sequences were aligned using MAFFT v7.309. Jalview v2.10.1 was used to trim the alignment and to look for reverse complemented sequences. Maximum likelihood-based phylogenetic analyses were performed using FastTree 2.1 software (with parameter […]

library_books

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

2018
MBio
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] nd their mammalian hosts. Data set 1 included 43 single-copy orthologs, and data set 2 included 10 genes. Multiple alignments were generated using MUSCLE (), manually inspected for inconsistencies in Jalview (), and concatenated. The best-fitting substitution model was the GTR+G model as estimated by jModel v.2.1.7 () using the corrected Akaike information criterion. Divergence times were estimate […]

library_books

Involvement of Met and Kr h1 in JH Mediated Reproduction of Female Bactrocera dorsalis (Hendel)

2018
Front Physiol
PMCID: 5945869
PMID: 29780329
DOI: 10.3389/fphys.2018.00482

[…] protein sequences from various species were downloaded from the National Center for Biotechnology Information web server and aligned with sequences of BdKr-h1 and BdMet in ClustalX 2 software () and JalView 2.9. A phylogenetic tree of these sequences was constructed by neighbor joining in 5.0 () with 1,000 bootstrap replicates. In addition, the online software tool ProtParam was used to predict t […]

call_split

Antibodies to the Glycoprotein GP2 Subunit Cross React between Old and New World Arenaviruses

2018
PMCID: 5932378
PMID: 29720525
DOI: 10.1128/mSphere.00189-18
call_split See protocol

[…] d amino acid sequences were extracted and labeled with short names as indicated below. A multiple sequence alignment (MSA) was generated using Clustal Omega, and the alignment file was analyzed using Jalview. Percent identity per position was then determined in Jalview as the percentage of utilized viral sequences that share the Lassa virus amino acid at each position. These percent identity value […]

library_books

Characterization of a novel organic solute transporter homologue from Clonorchis sinensis

2018
PLoS Negl Trop Dis
PMCID: 5942847
PMID: 29702646
DOI: 10.1371/journal.pntd.0006459

[…] atabase []. Multiple sequence alignments were carried out with the parameters of G-INS-i method, unalign level of 0.8, and BLOSUM30 scoring matrix using MAFFT ver. 7.394 [], and were visualized using Jalview []. A phylogenetic tree of homologous proteins was constructed using maximum parsimony methods of MEGA ver. 6.06 []. The probability of clustering with taxa was calculated using bootstrap test […]

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Jalview institution(s)
School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee, UK

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