LALIGN protocols

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LALIGN statistics

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Associated diseases

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LALIGN specifications

Information


Unique identifier OMICS_15830
Name LALIGN
Interface Web user interface
Restrictions to use None
Input data A query sequence
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

LALIGN in pipelines

 (16)
2018
PMCID: 5749712
PMID: 29293521
DOI: 10.1371/journal.pone.0189673

[…] sequence and changes made by routine improvements to the annotation pipeline., the replication origin, oric, was found by ori-finder []. similarity of (deduced) protein sequences was monitored with lalign version 36.3.5e [], internal repeat sequences were detected with internal repeats finder [], duf11 was located with myhits [] and putative promoters located by pattern locator []. prophage […]

2018
PMCID: 5826349
PMID: 29515563
DOI: 10.3389/fmicb.2018.00312

[…] sav_3491 (s. avermitilis), sven15_3779 (s. venezuelae), sgr_3904 (s. griseus), and sclav_3143/ sclav_3144 (s. clavuligerus). amino acid similarities were estimated using the software package lalign (http://www.ch.embnet.org/software/lalign_form.html)., the 46 genes significantly down-regulated in the δsco4117 mutant were grouped into 33 putative operons (supplementary table ). a library […]

2017
PMCID: 5343035
PMID: 28337212
DOI: 10.3389/fpls.2017.00305

[…] and transition weight 0.5)., due to the presence of a single member representing ttg1 in norway spruce and arabidopsis, the construction of a phylogenetic tree was not possible and we used the lalign analysis (http://www.ch.embnet.org/software/lalign_form.html) to calculate the identity and similarity between the protein sequences of our norway spruce candidate, pawd40-1, and atttg1., […]

2017
PMCID: 5577575
PMID: 28777321
DOI: 10.3390/toxins9080241

[…] used for multiple alignments of nucleotide and amino acid sequences of selw and sea. the pairwise alignment of nucleotide and amino acid sequences and the calculation of identity were performed by lalign server. nucleotide sequences of selw of 16 s. aureus isolates were deposited in the genbank database under accession numbers kx655702–kx655717., nuclease gene and orfx-cas1 sequences of an s. […]

2017
PMCID: 5609105
PMID: 28970842
DOI: 10.3389/fpls.2017.01591

[…] blastp and blastx suites were used to perform similarity searches in the predicted proteome database. protein sequence identity between the closest vvidreba1s homologs were performed by using the lalign program., multiple alignment analysis was performed at the swiss embnet node web server using clustalw and boxshade tools, respectively. the prediction of ubiquitination and sumoylation sites […]


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LALIGN in publications

 (111)
PMCID: 5877779
PMID: 29558430
DOI: 10.3390/ijms19030918

[…] (tms) were calculated by applying the boltzmann sigmoidal equation in prism5 (graphpad software, la jolla, ca, usa)., the amino acid sequence identity and similarity analyses were carried out with lalign (https://embnet.vital-it.ch/software/lalign_form.html) by applying local alignment method using default settings, i.e., blosum50 scoring matrix, 3 as number of reported sub-alignments, 10.0 […]

PMCID: 5881534
PMID: 29632815
DOI: 10.1002/2211-5463.12401

[…] retrieved according to previous studies , , , , . sequences were aligned by clustalw , and the conserved domains were identified as previously described . sequence identity was calculated using the lalign program (http://www.ch.embnet.org/software/lalign_form.html). protein tertiary structure was predicted using the raptorx structure prediction server (http://raptorx.uchicago.edu/) , […]

PMCID: 5829100
PMID: 29527191
DOI: 10.3389/fmicb.2018.00034

[…] identification of closely related strains to s211 was performed based on basic local alignment search tool (blast) searches. 16s rrna gene sequences were aligned with t-coffee (v11.00.8cbe486) using lalign_pair and slow_pair alignments (weng et al., ). the phylogenetic tree was reconstructed using the bayesian inference method implemented in the mrbayes program (v3.2.3). the number […]

PMCID: 5826349
PMID: 29515563
DOI: 10.3389/fmicb.2018.00312

[…] sav_3491 (s. avermitilis), sven15_3779 (s. venezuelae), sgr_3904 (s. griseus), and sclav_3143/ sclav_3144 (s. clavuligerus). amino acid similarities were estimated using the software package lalign (http://www.ch.embnet.org/software/lalign_form.html)., the 46 genes significantly down-regulated in the δsco4117 mutant were grouped into 33 putative operons (supplementary table ). a library […]

PMCID: 5816542
PMID: 29467823
DOI: 10.1186/s13068-018-1039-6

[…] replacement using phaser [] using residues 138–500 of pdb entry 3zmr as the search model [], which align to residues 106–464 of cjgh5d, with which they share 38% identity (using the program lalign from the fasta package []). the structure was built automatically using buccaneer [] and refined using cycles of manual model rebuilding using coot [] followed by refinement with refmac [], […]


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LALIGN institution(s)
Department of Computer Science, Michigan Technological University, Houghton, MI, USA; Department of Computer Science, The Pennsylvania State University, University Park, PA, USA
LALIGN funding source(s)
This work was supported by Grant R01 LM05110 form the National Library of Medicine.

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