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Analyses for Study 20124

Citation title: "Comparative genomic analysis of the flagellin glycosylation island of the Gram-positive thermophile Geobacillus".

Study name: "Comparative genomic analysis of the flagellin glycosylation island of the Gram-positive thermophile Geobacillus".

This study is part of submission 20124 (Status: Published).

Analyses

Analysis 1

Analysis details

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Notes

Input data

1 Input object(s)

Analysis step

Figure 3: Maximum Likelihood tree on basis of recN nucleotide sequence alignment to show the presence/absence of flagellin glycosylation islands among Geobacillus spp. --

Step details

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Notes

Software used

Name
Version
Description
Algorithm
Commands
The recN Maximum Likelihood trees were constructed with the Molecular Evolutionary Genetics Analysis (MEGA) v. 7.0.14 software package, using the Tamura-Nei evolutionary model, complete gap deletion, nearest-neighbour-interchange ML heuristic method and bootstrap analysis (n = 1,000).

Output data

1 Output object(s)

Analysis 2

Analysis details

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Input data

1 Input object(s)

Analysis step

Figure 4: Maximum Likelihood tree on basis of recN nucleotide sequence alignment to contrast against FGI typing UPGMA tree --

Step details

Name
Notes

Software used

Name
Version
Description
Algorithm
Commands
The recN Maximum Likelihood trees were constructed with the Molecular Evolutionary Genetics Analysis (MEGA) v. 7.0.14 software package [64], using the Tamura-Nei evolutionary model, complete gap deletion, nearest-neighbour-interchange ML heuristic method and bootstrap analysis (n = 1,000).

Output data

1 Output object(s)

Analysis 3

Analysis details

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Notes

Input data

1 Input object(s)

Analysis step

Supplementary Figure S2: Maximum likelihood phylogeny of the concatenated PseC and PseI amino acid sequences --

Output data

1 Output object(s)

Analysis 4

Analysis details

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Notes

Input data

1 Input object(s)

Analysis step

Figure 4: Conversion into distance matrix of data on presence/absence of protein orthologues within the Geobacillus flagellin glycosylation island --

Step details

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Notes

Software used

Name
Version
Description
Algorithm
Commands
The presence/absence matrix was used to generate a distance matrix using Bionumerics v 6.6 (Applied Maths N.V., Belgium) using absolute values and Pearson?s correlation.

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

Figure 4: UPGMA of distance matrix based on presence/absence of protein orthologues within the Geobacillus flagellin glycosylation island --

Output data