Kalign protocols

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


Maintainer


  • person_outline Timo Lassmann <>

Kalign IN pipelines

 (12)
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 (38), and the multiple protein sequence alignment was performed with kalign2 (39). the alignment was manually validated and corrected with seaview (40). this allowed to align the nucleotide sequences with tranalign software (38). nucleotide sites for the phylogeny […]

2017
PMCID: 5522442
PMID: 28733600
DOI: 10.1038/s41598-017-06598-x

[…] and onekp30. the cleavage site of the signal peptide in the precursor sequence was determined by signalp 4.050. the primary amino acid sequence and precursor sequence alignments were performed using kalign51. neighbor-joining clustering analysis was performed on mega 6.052, and a phylogenetic tree was constructed using a bootstrap test of 1000 replicates. the phylogenetic tree was displayed […]

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, 2005). visual alignment consensus was built at 70% threshold. relationships among pila1-a4 genes were inferred by phyml (guindon et al., 2009) […]

2017
PMCID: 5750628
PMID: 29073736
DOI: 10.3390/plants6040052

[…] described to be unique to isoprene synthase proteins (isps), differentiating them from related homologous terpene synthases (tps) [63]., clustalw [102] (k-align, http://www.ebi.ac.uk/tools/msa/kalign/, european bioinformatics institute, embl-ebi) was used for multiple sequence alignment of the 18s rrna dna sequence and isoprene synthase protein sequence. the phylogenetic trees of the dna […]

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 [35] 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 […]

Kalign institution(s)
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden

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