Kalign protocols

View Kalign computational protocol

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Popular tool citations

chevron_left Multiple nucleotide sequence alignment Multiple structure alignment chevron_right
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Associated diseases

Associated diseases

Kalign specifications

Information


Unique identifier OMICS_00978
Name Kalign
Interface Web user interface, Application programming interface
Restrictions to use None
Input data Protein or nucleic acid sequences
Input format GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP, UniProtKB/Swiss-Prot
Output data Sequence alignment
Output format FASTA, MACSIM, ClustalW
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Erik Sonnhammer <>
  • person_outline Timo Lassmann <>

Publications for Kalign

Kalign in pipelines

 (19)
2018
PMCID: 5785829
PMID: 29416569
DOI: 10.1186/s13100-018-0109-4

[…] complete h. pylori genome sequences obtained from the ncbi [, ] or patric [, ]. sequences were compared in pairwise and multiple sequence alignments as appropriate (needle/stretcher and clustalomega/kalign [] respectively, accessible from []), then manually re-annotated to establish precise definition of coding sequence and full gene content using bioedit [, ] and the suite of analysis tools […]

2017
PMCID: 5472674
PMID: 28670580
DOI: 10.3389/fvets.2017.00092

[…] of the dpol and the tk genes of bohv-4-fmv were used as the query sequence. dna sequences were then translated with transeq (), and the multiple protein sequence alignment was performed with kalign2 (). the alignment was manually validated and corrected with seaview (). this allowed to align the nucleotide sequences with tranalign software (). nucleotide sites for the phylogeny […]

2017
PMCID: 5512222
PMID: 28559295
DOI: 10.1128/JB.00245-17

[…] and s = 1.2. the hhpred program was used for profile-profile searches (). structure similarity searches were performed with the dalilite program (, ). multiple-sequence alignments were built by the kalign () and pcma () programs, followed by manual adjustments on the basis of profile-profile and structural alignments. secondary structures were predicted with the jpred program (). for previously […]

2017
PMCID: 5529391
PMID: 28798737
DOI: 10.3389/fmicb.2017.01410

[…] competence (16 genes) to t. thermophilus hb27 were used as reference for extracting competence associated genes from individual genomes using blast. pila1-a4 genes were aligned using hirschberg (kalign) algorithm (lassmann and sonnhammer, ). visual alignment consensus was built at 70% threshold. relationships among pila1-a4 genes were inferred by phyml (guindon et al., ) maximum-likelihood […]

2016
PMCID: 4960868
PMID: 27457073
DOI: 10.1186/s13742-016-0137-2

[…] to the whole gene (not including flanking sequences). because of high error rates with minion sequence data, we noticed a high rate of false positive genes. to reduce false positives, we used kalign2 [] to perform a multiple alignment of reads that were aligned to the same gene. the consensus sequence resulting from the multiple alignment was then compared with the gene sequence using […]


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Kalign in publications

 (165)
PMCID: 5908168
PMID: 29672618
DOI: 10.1371/journal.pone.0196052

[…] tree was constructed using all available sequences of herpetomonas species retrieved from genbank with phytomonas spp. as an outgroup (). alignments for phylogenetic analysis were generated in kalign []; the ambiguously aligned positions in the trimmed alignment were removed manually in bioedit (ibis therapeutics, carlsbad, us). the final dataset contained 46 taxa and 1,988 nucleotide […]

PMCID: 5906684
PMID: 29670199
DOI: 10.1038/s41598-018-24467-z

[…] (against: pdb70_12feb17, scop95_v1.75b and pfama_31.0, using msa generation method hhblits run for 5 iterations, e-value threshold of 0.001). multiple sequence alignments were constructed using kalign followed by manual corrections based on structural alignments. sequence similarity-based clustering was performed using the blastclust program […]

PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] aligned with 14 different methods: l-ins-i, e-ins-i and g-ins-i strategies of mafft v7; psi-coffee, expresso; t-coffee; probcons v1.12; probalign v1.3; prank; muscle v3.7; msaprobs v0.9.7; kalign; dialign-tx; and clustal omega. the 10 best alignments were selected after evaluation with mumsa based on multiple overlap (mos) and average overlap (aos) scores. alignments with mos […]

PMCID: 5915158
PMID: 29707150
DOI: 10.18632/oncotarget.24894

[…] a list of sequences used in this study is provided in . the multi-species peptide sequences were from ensembl (http://www.ensembl.org). alignment of peptide sequences was performed using the kalign server (http://msa.sbc.su.se/cgi-bin/msa.cgi). the comparisons were computed as local alignments using the default parameters of the program. phylogenetic tree comparisons were made using […]

PMCID: 5858815
PMID: 29554153
DOI: 10.1371/journal.pone.0194664

[…] of an annotated sequence, or (c) at least 95% identical homology with annotated a. aegypti ncbi refseq. all primer pairs were designed on the primer3 software (bioinfo.ut.ee/primer3-0.4.0/). the kalign nucleic acid alignment software (http://www.ebi.ac.uk/tools/msa/kalign/) was used to specify for regions spanning exon-exon boundaries. restrictive parameters for primer selection were: […]


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Kalign institution(s)
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Stockholm Bioinformatics Centre, Albanova, Stockholm University, Stockholm, Sweden

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