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Moreover, in the second level, the TF can be manually refined and the volume can be further inspected through geometric tools.
We reconstructed a total of 73 vent-specific MAGs manually refined and quality-controlled from 12 metagenomes from both Piccard and Von Damm (Supplementary Fig. 2; Supplementary Data 2) with a minimum completeness of 70% and maximum redundancy of 10%.
The resulting alignment was manually refined and trimmed using BioEdit sequence-editing software [ 99].
This alignment was then manually refined and end trimmed using BioEdit version 7.0.5.3 [ 48].
Alignments were manually refined, and poorly aligned regions were eliminated manually.
The preliminary assemblies were not manually refined and directly submitted to the following genome alignment step.
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All these alignments were inspected, manually refined if required, and are available upon request.
16S sequences were obtained for publically available Paenibacillacae from the NCBI Nucleotide database and aligned using ClustalΩ [ 106] and manually refined within MEGA6 [ 44].
For phylogenetic analysis of the Cox proteins, TBLASTX searches were carried out, the corresponding sequences recovered from GenBank and a multiple alignment generated using Clustal X and manually refined as mentioned above.
Initial sequence alignments were generated in ClustalX2 [40] and manually refined from 3D alignments of available crystal structures for hsp15.5, scL30e, hmL7Ae, scSnu13p, hsGadd45g and generated models of hsSBP2_RBD and xtGadd45a.
Genes were assigned to functional categories using the yeast Gene Ontology (GO) tool "GO Slim Mapper" and further manually refined according to annotations of the BIOBASE Knowledge Library Proteome and the Saccharomyces Genome Database (SGD).
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