Sequence Harmony protocols

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Sequence Harmony statistics

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Sequence Harmony specifications


Unique identifier OMICS_07160
Name Sequence Harmony
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for Sequence Harmony

Sequence Harmony in pipeline

PMCID: 3418547
PMID: 22569235
DOI: 10.1186/1745-6150-7-14

[…] by prottest (v2.4) []., in order to identify the specific amino acids that allow the discrimination between the two mitochondrial rf1 homologous subfamilies, we submitted our alignment to sequence harmony [] and selected the positions that are, in the vertebrates, perfectly conserved within mtrf1 and within mtrf1a, but that are different between them., all models were built using […]

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Sequence Harmony in publications

PMCID: 5548252
PMID: 28642127
DOI: 10.1016/j.bbagen.2017.06.014

[…] by removing binders from alpaca and separating llama- and dromedary-derived sequences. subtype-specific positions were determined using the web-server with a sequence harmony cut off value of 0.7. for , sequence harmony values were inverted., crystallographic data and coordinate files were retrieved from the rcsb protein database (pdb; june 2016). […]

PMCID: 5112890
PMID: 27851829
DOI: 10.1371/journal.ppat.1005989

[…] and implemented a novel approach for statistically quantifying early env diversity. first, fasta amino acid alignments of the t/f envs and early envs from the same patient were subjected to sequence harmony analysis to identify amino acid positions that were significantly different between the two groups of sequences (z-score ≤ -3) [,,]. as a proof of concept for this approach, we first […]

PMCID: 4948766
PMID: 27427956
DOI: 10.1371/journal.pone.0157895

[…] members of the lyr family: lyrm2, lyrm3, lyrm5, lyrm7 and acn9, in total containing 617 sequences. the combined alignment, again restricted to positions that are present in isd11, was analyzed with sequence harmony [] to identify the positions most specific to isd11., l-cysteine desulfurase activity was quantified by the methylene blue method [] following the protocol previously described []. […]

PMCID: 4599308
PMID: 26449222
DOI: 10.1186/s12859-015-0758-y

[…] sum is over all 20 amino acids. a low sequence entropy s i represents higher evolutionary conservation. we calculated average entropies for each pair group for comparison among varied positions., sequence harmony [, ], an entropy based method, is applied to detect the compositional differences between subgroups. the program is accessible as a web-server from: […]

PMCID: 4695503
PMID: 26752808
DOI: 10.1007/s11105-015-0883-9

[…] by costa et al. (). due to the broad diversity in the first 100 amino acids of the aox protein sequences for comparative analysis the conserved fragment of aox sequence (101–354 aa) was used. for ‘sequence harmony’ (sh) methodology (feenstra et al. ) the set of 67 aox2a–c subtype proteins (prepared by costa et al. ()) and seqharm version 1.1 ( […]

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Sequence Harmony reviews

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