Expansin Engineering Database

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

Featured Dataverses

In order to use this feature you must have at least one published or linked dataverse.

Publish Dataverse

Are you sure you want to publish your dataverse? Once you do so it must remain published.

Publish Dataverse

This dataverse cannot be published because the dataverse it is in has not been published.

Delete Dataverse

Are you sure you want to delete your dataverse? You cannot undelete this dataverse.

1 to 10 of 28 Results

Update_2_Centroids_USEARCH.tab Jan 30, 2020 - Query sequences for the update of the ExED Tabular Data - 505 B - 1 Variables, 25 Observations - UNF:6:eFcDsa8udm3F11lB7M2q6w== Tabular file with headers: sequence identifier from the Expansin Engineering Database (1st column) and NCBI accession.version (2nd column). This file lists the sequence accessions used in the first update of the ExED.
Update_2_Centroids_USEARCH.fasta Jan 30, 2020 - Query sequences for the update of the ExED Unknown - 6.5 KB - MD5: 5ae0036abf33f3585e5629a8337b7039 Seed (query) sequences for the first update of the ExED (USEARCH centroid sequences). Protein sequences are given in FASTA format with one line per sequence. Headers correspond to sequence identifiers of the Expansin Engineering Database.
Update_1_Seed_sequences_Hfams_1-25.fasta Jan 30, 2020 - Query sequences for the update of the ExED Unknown - 8.7 KB - MD5: 4f5de838715758c51a8cf33de96da0e8 Seed (query) sequences for the initial setup of the ExED. Protein sequences are given in FASTA format. Headers correspond to sequence identifiers in the style of UniprotKB.
Taxonomic_analysis.tab Apr 9, 2020 - Occurrence of expansins in the tree of life Tabular Data - 4.0 KB - 6 Variables, 90 Observations - UNF:6:eK0oQia4QiaiEO0m1BJFeA== Tabular comparison between the occurrences of expansins in different taxa as reported in the Expansin Engineering Database (ExED) and Chase et al. (2020): Name of the taxonomic superkingdom; Name of the (major) taxonomic group reported in Chase et al. 2020; Lineage contains ex...
Sfams_123_210-300_90_50.graphml Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues GraphML Network Data - 85.9 MB - MD5: 6b7c3ee5702bf65837900503ef335e54 Protein sequence network for N-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database, for sequences with length between 210 and 300 residues.The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ U...
Sfam_123_Cdomain_90_60.graphml Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues GraphML Network Data - 20.8 MB - MD5: 1bcf30f501153632979c2e032fe5a497 Protein sequence network for C-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database. The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ UCLUST) connected by at least 60% pairwise sequence iden...
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/).
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.
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.
Ndomains_1234_CBM_09_60identity.graphml Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues GraphML Network Data - 25.2 MB - MD5: dd85b921f70e99ae9cbffc2156be55c0 Protein sequence network for N-terminal expansin domains from the bacterial, fungal, plant and N-terminal domains superfamily from the Expansin Engineering Database. The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ UCLUST) connected by at least 60% pa...

Update_2_Centroids_USEARCH.tab

Jan 30, 2020 - Query sequences for the update of the ExED

Tabular Data - 505 B - 1 Variables, 25 Observations -

Tabular file with headers: sequence identifier from the Expansin Engineering Database (1st column) and NCBI accession.version (2nd column). This file lists the sequence accessions used in the first update of the ExED.

Update_2_Centroids_USEARCH.fasta

Jan 30, 2020 - Query sequences for the update of the ExED

Unknown - 6.5 KB -

Seed (query) sequences for the first update of the ExED (USEARCH centroid sequences). Protein sequences are given in FASTA format with one line per sequence. Headers correspond to sequence identifiers of the Expansin Engineering Database.

Update_1_Seed_sequences_Hfams_1-25.fasta

Jan 30, 2020 - Query sequences for the update of the ExED

Unknown - 8.7 KB -

Seed (query) sequences for the initial setup of the ExED. Protein sequences are given in FASTA format. Headers correspond to sequence identifiers in the style of UniprotKB.

Taxonomic_analysis.tab

Apr 9, 2020 - Occurrence of expansins in the tree of life

Tabular Data - 4.0 KB - 6 Variables, 90 Observations -

Tabular comparison between the occurrences of expansins in different taxa as reported in the Expansin Engineering Database (ExED) and Chase et al. (2020): Name of the taxonomic superkingdom; Name of the (major) taxonomic group reported in Chase et al. 2020; Lineage contains ex...

Sfams_123_210-300_90_50.graphml

Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues

GraphML Network Data - 85.9 MB -

Protein sequence network for N-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database, for sequences with length between 210 and 300 residues.The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ U...

Sfam_123_Cdomain_90_60.graphml

Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues

GraphML Network Data - 20.8 MB -

Protein sequence network for C-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database. The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ UCLUST) connected by at least 60% pairwise sequence iden...

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/).

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.

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.

Ndomains_1234_CBM_09_60identity.graphml

Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues

GraphML Network Data - 25.2 MB -

Protein sequence network for N-terminal expansin domains from the bacterial, fungal, plant and N-terminal domains superfamily from the Expansin Engineering Database. The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ UCLUST) connected by at least 60% pa...

Add Data

Share Dataverse

Link Dataverse

Reset Modifications