PROMALS3D pipeline

PROMALS3D specifications


Unique identifier OMICS_03731
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PROMALS3D

PROMALS3D citations

PMCID: 5349461

[…] and used for detection of protein domain conservation and phylogenetic analysis. experimental features human, e.coli and archaea protein helicase sequences were aligned using tcoffee or promals3d..conserved motifs were detected from multiple sequence alignments using weblogo software. phylogenetic analysis were performed using maximum likelihood methods or bayesian methods […]

PMCID: 5311999

[…] distinct domains between homologous groups. mj0277 homologs had tpp_ahas and prl06276 while mj0663 homologs had tpp_enzymes super family and ilvb domains instead. multiple sequence alignment using promals3d showed the mj0277 homologs a tighter group than mj0663 and its homologs. phylip showed these homologous groups as evolutionarily distinct yet equal distance from bacterial als proteins […]

PMCID: 5311999

[…] (rps-blast), a position-specific iterative (psi)-blast variant, to establish position-specific scoring matrices with the protein sequence [17]. together, pfam and cdd-blast examine protein domains., promals3d used whole protein sequences in fasta format for three multiple sequence alignments, one with mj0277 homologs only, one with mj0663 homologs only, and one with all proteins in table 1 plus […]

PROMALS3D institution(s)
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA

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