Running Clans For Protein Sequence Clustering

I am trying to run clans to cluster ~100 protein sequences. However it does not seem to converge. I am wondering how long it usually takes to run clustering.

clustering

• 3,588 views • link

updated 9.5 years ago by krutikeshpatel11 •

• written 12.5 years ago by Pappu

1 answer

I guess it will never stop because force vectors are used, however the graph may come at equilibrium after some time. You can find clusters (convex,network or linkage methods available) by going to >Windows (drop down) >find clusters option.I hope it solves answers the question.

• 0 views • link

written 9.5 years ago by krutikeshpatel11 •

More posts like this

Export CLANS clusters in separate multifasta files
written 6.1 years ago by hazirliver •

Hi! I use CLANS to cluster protein sequences. I need to export the clusters found using CLANS into separate multifasta files, where each file will …
Gene ontology clustering
written 9.2 years ago by niutster

Hi, I performed Gene ontology for a genes list containing near 1000 genes but result contains near 100 biological process (all are in significant p.value), …
Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
written 11.0 years ago by BDK_compbio

I used both BlastClust and CD-HIT for clustering protein sequences. The output of CD-HIT looks good but it is creating too many clusters (6000 clusters …
Homologous Sequence Identity
written 12.4 years ago by Pappu

I am trying to figure out how sequences of two protein families are conserved in various species. I have two fasta files containing sequences of …
Why Proteins Of Some Genomes Are More Stable
written 12.5 years ago by Pappu

I am trying to find out why proteins from a few species are more stable than human proteins by analysing the DNA and protein sequences. …
Function Of Amino Acids In Protein Repeated Several Times
written 12.7 years ago by Pappu

I often encounter low complexity regions in protein sequences especially many repeats of the same amino acid. I saw some papers which suggest that it …
Why Does Mothur Require An Alignment Step Before Clustering?
written 12.9 years ago by vijay

Dear all, I am trying to cluster my sequence dataset so that I can determine the number of OTU's at various percent identities. I have …
Best Way To Check Topology Support For A Phylogenetic Tree
written 13.2 years ago by Pappu

I made phylogenetic tree using FastTree of an alignment ~2000 protein sequences. I am willing to know how the topology support for the branches can …
Constructing Phylogenetic Tree And Analysing Evolution Of A Protein
written 13.2 years ago by Pappu

I am trying to understand the evolution of a protein domain by constructing Phylogenetic tree and by analyzing its last common eukaryotic ancestor (LCEA). I …
Dowloading All Protein Sequences
written 13.4 years ago by Pappu

I downloaded the trembl database from uniprot website. But it does not seem to contaln all the protein sequences. I am wondering which database contains …