%0 Generic %1 buchholz2020expansin %A Buchholz, Patrick C. F. %D 2020 %K darus ubs_10003 ubs_20003 ubs_30187 unibibliografie %R 10.18419/darus-699 %T Expansin homologues in actinobacterial genomes from South Africa %X Hit sequences for putative expansins (or expansin domains) are reported from an exemplary genome screening. Five actinobacterial genomes were selected to show the application of the Expansin Engineering Database (ExED) for the identification of expansin domains. The original nucleic acid sequences were translated by the standard codon usage table implemented in the transeq tool from the EMBOSS software suite. The hmmscan tool from the HMMER software suite was used to scan the translated amino acid sequences with profile hidden Markov models (profile HMMs) representing the N- and C-terminal expansin domains. The hits from hmmscan were filtered by a minimal domain-based score of 35 and a minimal coverage of 75% (defined as the ratio of hit length without insertions divided by the length of the profile HMM). The matches for the profile HMMs of both expansin domains were extended to find the adjacent start methionine and stop codon along the contig sequence of each match. The first or last available amino acid position in a contig was used to extend the hits in case of a missing start or stop codon, respectively.

@misc{buchholz2020expansin, abstract = {Hit sequences for putative expansins (or expansin domains) are reported from an exemplary genome screening. Five actinobacterial genomes were selected to show the application of the Expansin Engineering Database (ExED) for the identification of expansin domains. The original nucleic acid sequences were translated by the standard codon usage table implemented in the transeq tool from the EMBOSS software suite. The hmmscan tool from the HMMER software suite was used to scan the translated amino acid sequences with profile hidden Markov models (profile HMMs) representing the N- and C-terminal expansin domains. The hits from hmmscan were filtered by a minimal domain-based score of 35 and a minimal coverage of 75% (defined as the ratio of hit length without insertions divided by the length of the profile HMM). The matches for the profile HMMs of both expansin domains were extended to find the adjacent start methionine and stop codon along the contig sequence of each match. The first or last available amino acid position in a contig was used to extend the hits in case of a missing start or stop codon, respectively.}, added-at = {2022-03-08T18:37:34.000+0100}, affiliation = {Buchholz, Patrick C. F./Universität Stuttgart}, author = {Buchholz, Patrick C. F.}, biburl = {https://puma.ub.uni-stuttgart.de/bibtex/21ffb852580f41f91434afcd34b988ad8/unibiblio}, doi = {10.18419/darus-699}, howpublished = {Dataset}, interhash = {b5ab28b596f39cbfded542a3c49a6978}, intrahash = {1ffb852580f41f91434afcd34b988ad8}, keywords = {darus ubs_10003 ubs_20003 ubs_30187 unibibliografie}, note = {Related to: Lohoff C., Buchholz P. C. F., Le Roes-Hill M. & Pleiss J. (2020). The Expansin Engineering Database: a navigation and classification tool for expansins and homologues. Proteins: Structure, Function, and Bioinformatics 89:2. doi: 10.1002/prot.26001}, orcid-numbers = {Buchholz, Patrick C. F./0000-0001-5967-3777}, timestamp = {2022-03-08T17:37:34.000+0100}, title = {Expansin homologues in actinobacterial genomes from South Africa}, year = 2020 }