Computational protocol: Analyses of Physcomitrella patens Ankyrin Repeat Proteins by Computational Approach

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Protocol publication

[…] The publicly available protein sequences of P. patens were downloaded from the JGI Phytozome database (first release of the moss genome annotation) [] and domain annotation of these proteins was done by InterProScan []. Then ANK proteins were screened by searching for the PF00023 domain using an in-house Perl script as described in a previous paper []. BLASTP was carried out with NCBI nonredundant protein database using the sequences retrieved from InterProScan as queries. After that, the candidate sequences were curated manually using available annotations in GenBank and existing literature. The molecular weights and isoelectric points were determined separately from online web server (http://www.bioinformatics.org/sms2/). Subcellular localization was predicted by the online web server of ProtComp 9.0 (http://www.softberry.com/berry.phtml?topic=protcomppl&group=help&subgroup=proloc). [...] The proteins were classified into different subgroups based on the presence of additional conserved domains other than the ANK domain as described previously [, ]. Phylogenetic tree file was constructed by the online webserver, SATCHMO-JS []; and the tree was visualized by the Molecular Evolutionary Genetics Analysis (MEGA) software version 4.1 []. In addition, synonymous and nonsynonymous substitution pattern were determined as described previously []. […]

Pipeline specifications

Software tools InterProScan, BLASTP, ProtComp, pRoloc, MEGA
Databases Phytozome
Applications Phylogenetics, Protein sequence analysis
Organisms Physcomitrella patens