What Softwares Can Be Used For Clustering Nucleic Acid Fragments??

Question

[Angel]

What kind of softwares can be used for clustering nucleic acid fragments??

[lh3]

This highly depends on your purpose and the type of your sequences. There is no single algorithm that solves every problem.

[lh3]

This highly depends on your purpose and the type of your sequences.

Answer 1

[Pawel Szczesny]

For clustering (that is grouping by similarity) I use often cd-hit. It has a special version designed to cluster fragments/reads from 454 sequencer: cd-hit-454.

If more fine grained clustering is necessary, you can use CLANS (visual clustering software on the basis of BLAST similarity).

Finally, if the group of sequences is similar you can do MSA, as Larry suggested.

[Larry_Parnell]

+1. Impossible to know if this is based on sequence reads or similar seqs for an MSA.

Answer 2

[Manu Prestat]

Another solution without MSA (by the way, I'm not sure that MSA is clustering):

you can build a similarity-based network (by using a usearch or blast all-against-all result file), and then apply a pruning algorithm like mcl or silix. This strategy is for me the most efficient way to have good clusters, but it is slower than using uclust or cd-hit.

[Larry_Parnell]

This is helpful +1. Long before there was software or even the thought of aligning numerous sequence reads, there was CLUSTALW, aprogram designed to perform an MSA and draw a dendrogram, which clustered similar sequences in visual space. Whether that historical precedent is now lost to sequence assembly is a matter for friendly debate, preferably over coffee/tea/beer.

Answer 3

[Larry_Parnell]

Clustering is distinct from assembling (sequence reads) and implies a multiple sequence alignment (MSA). An MSA can be used as input for phylogenetic analysis, the output of which resembles a tree showing clusters of taxa (sequences) of similarity on branches.

You can perform an MSA with CLUSTAL/CLUSTALW, TCOFFEE or MUSCLE or any of several other such algorithms. Many have web-accessibility.

[Larry_Parnell]

Your question does not state structure or sequence: What kind of softwares [sic] can be used for clustering nucleic acid fragments?

[Angel]

@larry_Parnell i was asking clustering based on nucleic acid structures not sequence..