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Part 1: Document Description
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Citation |
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Title: |
Profile hidden Markov models of the ExED |
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Identification Number: |
doi:10.18419/darus-623 |
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Distributor: |
DaRUS |
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Date of Distribution: |
2020-01-30 |
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Version: |
1 |
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Bibliographic Citation: |
Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", https://doi.org/10.18419/darus-623, DaRUS, V1 |
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Citation |
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Title: |
Profile hidden Markov models of the ExED |
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Alternative Title: |
Profile hidden Markov models of the Expansin Engineering Database |
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Identification Number: |
doi:10.18419/darus-623 |
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Authoring Entity: |
Lohoff, Caroline (Universität Stuttgart) |
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Distributor: |
DaRUS |
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Access Authority: |
Pleiss, Jürgen |
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Depositor: |
Buchholz, Patrick C. F. |
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Date of Deposit: |
2020-01-27 |
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Holdings Information: |
https://doi.org/10.18419/darus-623 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, protein sequence, multiple sequence alignment, profile hidden Markov model, amino acid sequence, protein domain |
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Abstract: |
Profile hidden Markov models and their underlying multiple sequence alignments for the N- and C-terminal protein domains of expansins. |
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Notes: |
A profile hidden Markov model (HMM) was derived for each expansin domain from a multiple sequence alignment built from 28 representative protein sequences. The profile HMMs for the N- and C-terminal expansin domain were built by HMMER from multiple sequence alignments (structure-guided). Based on the alignment and on annotations of secondary structures in the Pfam database (entries PF03330.17 for the N-terminal domain and PF01357.20 for the C-terminal domain), the respective domains were manually retrieved. |
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Methodology and Processing |
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Sources Statement |
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Data Sources: |
Expansin Engineering Database (<a href="https://exed.biocatnet.de/">https://exed.biocatnet.de/</a>) |
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Pfam Database (<a href="https://pfam.xfam.org/">https://pfam.xfam.org/</a>) |
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RCSB Protein Data Bank (<a href="https://www.rcsb.org/">https://www.rcsb.org/</a>) |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
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. |
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Identification Number: |
10.1002/prot.26001 |
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Bibliographic Citation: |
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. |
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Label: |
Expansins_CterminalDomain_2.aln |
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Text: |
Clustal alignment for the C-terminal expansin domain |
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Notes: |
application/octet-stream |
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Label: |
Expansins_CterminalDomain_2.hmm |
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Text: |
Profile hidden Markov model in HMMER format for the C-terminal expansin domain |
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Notes: |
application/octet-stream |
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Label: |
Expansins_CterminalDomain_2.sto |
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Text: |
Stockholm alignment for the C-terminal expansin domain |
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Notes: |
application/octet-stream |
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Label: |
Expansins_NterminalDomain_9.aln |
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Text: |
Clustal alignment for the N-terminal expansin domain |
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Notes: |
application/octet-stream |
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Label: |
Expansins_NterminalDomain_9.hmm |
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Text: |
Profile hidden Markov model in HMMER format for the N-terminal expansin domain |
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Notes: |
application/octet-stream |
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Label: |
Expansins_NterminalDomain_9.sto |
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Text: |
Stockholm alignment for the N-terminal expansin domain |
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Notes: |
application/octet-stream |