michaelting/BioE144L

structural_phylogenomics:

Structural phylogenomic analysis of an alkyldihydroxyacetonephosphate synthase protein from C. elegans (GI:17556096, UniProt:ADAS_CAEEL). Analysis indicated that PDB structure 2UUU fit most closely with the query, and was supported by conservation of domains and function across orthologous clades denoted in phylogenetic trees.

• Files:
  • hmmscoreparser.py - file for parsing GI accessions from HMM score files in tabular form
  • Sequence data in FASTA format
  • HMM scoring files
  • MSA files produced using MAFFT and visualized in Belvu
  • Phylogenetic trees constructed using FastTree and visualized with ETE2 in Python

arath_gpcr:

Bioinformatics analyses for a putative GPCR in Arabidopsis thaliana Uniprot:O04714 (GCR1_ARATH). Analyses were performed to find evidence for or against the presence of a G protein-coupled receptor in Arabidopsis.

functional_site_prediction:

Analysis of protein functional site prediction methods using a consensus webserver approach.