Expansin Engineering Database

Supporting information and original files for bioinformatic investigations using the Expansin Engineering Database (https://exed.biocatnet.de/)

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1 to 7 of 7 Results

Expansin domains in CBM63 sequences Jun 16, 2020 Lohoff, Caroline, 2020, "Expansin domains in CBM63 sequences", https://doi.org/10.18419/DARUS-625, DaRUS, V2, UNF:6:p+wfgXpfeyT0/kJm49wLTA== [fileUNF] The occurrence of N- and C-terminal expansin domains in CBM63 sequences from the CAZy database. Protein sequences are represented by NCBI accessions. Expansin domains were annotated with the hmmscan command from the HMMER software package. The hits were filtered by a minimal domain-based score of 35 or 20 (chosen after comparison with HMMER’s domai...
Conserved positions in expansin homologues Apr 9, 2020 Lohoff, Caroline, 2020, "Conserved positions in expansin homologues", https://doi.org/10.18419/DARUS-735, DaRUS, V1, UNF:6:HemykMznkJ0tyrf89mswkg== [fileUNF] Conserved positions in the N- and C-terminal expansin domains of different groups from the Expansin Engineering Database (occurring in at least 70% of the annotated sequence entries). The expansin domains were annotated using hmmscan (from the HMMER software suite) against all sequence entries in the Expansin Engineering Database.
Expansin homologues in actinobacterial genomes from South Africa Apr 9, 2020 Buchholz, Patrick C. F., 2020, "Expansin homologues in actinobacterial genomes from South Africa", https://doi.org/10.18419/DARUS-699, DaRUS, V1 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 i...
Occurrence of expansins in the tree of life Apr 9, 2020 Lohoff, Caroline, 2020, "Occurrence of expansins in the tree of life", https://doi.org/10.18419/DARUS-693, DaRUS, V1, UNF:6:eK0oQia4QiaiEO0m1BJFeA== [fileUNF] Comparison between expansins found in the Expansin Engineering Database (ExED) and literature.
GraphML files for protein sequence networks of expansin homologues Jan 30, 2020 Lohoff, Caroline, 2020, "GraphML files for protein sequence networks of expansin homologues", https://doi.org/10.18419/DARUS-624, DaRUS, V1 GraphML files for undirected weighted graphs with nodes that represent protein sequences of expansin homologues. Protein sequences were clustered by a threshold of sequence identity to derive representative sequences.Pairwise sequence identity between two sequences was derived from global Needleman-Wunsch alignment. Protein sequence networks were g...
Profile hidden Markov models of the ExED Jan 30, 2020 Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", https://doi.org/10.18419/DARUS-623, DaRUS, V1 Profile hidden Markov models and their underlying multiple sequence alignments for the N- and C-terminal protein domains of expansins.
Query sequences for the update of the ExED Jan 30, 2020 Lohoff, Caroline; Buchholz, Patrick C. F., 2020, "Query sequences for the update of the ExED", https://doi.org/10.18419/DARUS-622, DaRUS, V1, UNF:6:eFcDsa8udm3F11lB7M2q6w== [fileUNF] Query sequences for the individual BLAST searches used to update the Expansin Engineering Database (ExED, https://exed.biocatnet.de/).

Expansin domains in CBM63 sequences

Jun 16, 2020

Lohoff, Caroline, 2020, "Expansin domains in CBM63 sequences", https://doi.org/10.18419/DARUS-625, DaRUS, V2, UNF:6:p+wfgXpfeyT0/kJm49wLTA== [fileUNF]

The occurrence of N- and C-terminal expansin domains in CBM63 sequences from the CAZy database. Protein sequences are represented by NCBI accessions. Expansin domains were annotated with the hmmscan command from the HMMER software package. The hits were filtered by a minimal domain-based score of 35 or 20 (chosen after comparison with HMMER’s domai...

Conserved positions in expansin homologues

Apr 9, 2020

Lohoff, Caroline, 2020, "Conserved positions in expansin homologues", https://doi.org/10.18419/DARUS-735, DaRUS, V1, UNF:6:HemykMznkJ0tyrf89mswkg== [fileUNF]

Conserved positions in the N- and C-terminal expansin domains of different groups from the Expansin Engineering Database (occurring in at least 70% of the annotated sequence entries). The expansin domains were annotated using hmmscan (from the HMMER software suite) against all sequence entries in the Expansin Engineering Database.

Expansin homologues in actinobacterial genomes from South Africa

Apr 9, 2020

Buchholz, Patrick C. F., 2020, "Expansin homologues in actinobacterial genomes from South Africa", https://doi.org/10.18419/DARUS-699, DaRUS, V1

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 i...

Occurrence of expansins in the tree of life

Apr 9, 2020

Lohoff, Caroline, 2020, "Occurrence of expansins in the tree of life", https://doi.org/10.18419/DARUS-693, DaRUS, V1, UNF:6:eK0oQia4QiaiEO0m1BJFeA== [fileUNF]

Comparison between expansins found in the Expansin Engineering Database (ExED) and literature.

GraphML files for protein sequence networks of expansin homologues

Jan 30, 2020

Lohoff, Caroline, 2020, "GraphML files for protein sequence networks of expansin homologues", https://doi.org/10.18419/DARUS-624, DaRUS, V1

GraphML files for undirected weighted graphs with nodes that represent protein sequences of expansin homologues. Protein sequences were clustered by a threshold of sequence identity to derive representative sequences.Pairwise sequence identity between two sequences was derived from global Needleman-Wunsch alignment. Protein sequence networks were g...

Profile hidden Markov models of the ExED

Jan 30, 2020

Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", https://doi.org/10.18419/DARUS-623, DaRUS, V1

Profile hidden Markov models and their underlying multiple sequence alignments for the N- and C-terminal protein domains of expansins.

Query sequences for the update of the ExED

Jan 30, 2020

Lohoff, Caroline; Buchholz, Patrick C. F., 2020, "Query sequences for the update of the ExED", https://doi.org/10.18419/DARUS-622, DaRUS, V1, UNF:6:eFcDsa8udm3F11lB7M2q6w== [fileUNF]

Query sequences for the individual BLAST searches used to update the Expansin Engineering Database (ExED, https://exed.biocatnet.de/).

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