FeatureMap3D protocols

View FeatureMap3D computational protocol

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FeatureMap3D specifications

Information


Unique identifier OMICS_25682
Name FeatureMap3D
Interface Web user interface
Restrictions to use None
Input data Some protein sequences.
Input format TSV, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anne Molgaard <>

Publication for FeatureMap3D

FeatureMap3D in pipeline

2009
PMCID: 2762064
PMID: 19828075
DOI: 10.1186/1471-2105-10-S12-S15

[…] splicing database, ensembl databank and protein data bank. primary data from these databases have been integrated and analyzed using the protein identifier cross-reference, blast, clustalw and featuremap3d software tools., a database has been developed to store the considered primary data and the results from their analysis; a system of perl scripts has been implemented to automatically […]


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FeatureMap3D in publications

 (3)
PMCID: 5809095
PMID: 29329287
DOI: 10.1371/journal.pntd.0006198

[…] for each denv-3 genotype as well as recent indonesian and southeast asian strains., amino acid changes mapping onto existing homologous structural data from protein data bank (pdb) was done by using featuremap3d (http://www.cbs.dtu.dk/services/) []. the multiple sequence alignment dataset was also used to check for the presence of recombination in our isolate by using the recombination detection […]

PMCID: 3208247
PMID: 21999571
DOI: 10.1186/1471-2164-12-505

[…] 131 primary tumors and 19 metastases []., first, the peptides corresponding to the unique sequences of the different isoforms were aligned against the protein data bank database by psiblast []. then featuremap3d [], pymol (molecular graphics system, delano, scientific system, llc, palo alto, ca), and scripts created for the analysis were used to analyze and visualize the structures and/or […]

PMCID: 2762064
PMID: 19828075
DOI: 10.1186/1471-2105-10-S12-S15

[…] in order to determine in which type of protein secondary structure each annotated residue of alternatively spiced isoforms is involved. data from the previous annotation step are processed using featuremap3d [], which uses blast to align a query sequence to pdb entries, thus predicting the structure of the input sequence. blast results from featuremap3d are stored in the featuremap3d_reports […]


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FeatureMap3D institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
FeatureMap3D funding source(s)
Supported by a grant from The Danish National Research Foundation and The Danish Research Agency.

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