T-Coffee Server
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T-RMSD
Allows fine-grained structural clustering of a given group of related protein domains (new)
Sequences input
Paste or upload your set of sequences in FASTA format
Sequences to align
Click here to use the sample file
- OR -
Click here to upload a file
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x
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Show more options
Structure(s) input
Upload your PDB structure if needed (Do NOT upload Confidential Data!)
PDB file
Click here to upload a file
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x
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PDB file
Click here to upload a file
[
x
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PDB file
Click here to upload a file
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x
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Library Computation
Select the methods you want to use to compute the library. T-Coffee uses various sequence and structure alignment methods to compile a collection of alignments known as a Library. Use this section to select the methods.
Pairwise Structual Methods
sap_pair
TMalign_pair
mustang_pair
Multiple Methods
pcma_msa
mafft_msa
clustalw_msa
dialigntx_msa
poa_msa
muscle_msa
probcons_msa
t_coffee_msa
amap_msa
kalign_msa
fsa_msa
probconsRNA_msa
mus4_msa
Pairwise Methods
best_pair4prot
fast_pair
clustalw_pair
lalign_id_pair
slow_pair
proba_pair
PDB structure selection
Specify which PDB structure (template) should be associated with which each sequence. The uploaded PDBs are automatically associated with their own sequence. Check the box to automatically fetch the templates, or fill the box and specify the sequence/template association
Enter your template
- OR -
Click here to upload a file
[
x
]
Automatically fetch pdb templates
MODE_PDB
Output options
Use this section to control the output format.
Case
upper
lower
keep
outorder
input
aligned
Alignment length
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T-Coffee Server is hosted by the Centre for Genomic Regulation (CRG) of Barcelona
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T-Coffee Server is hosted by the Centre for Genomic Regulation (CRG) of Barcelona
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