Aligning And Find Secondary Structures

Question

[saeid]

Hi I am a biologist not a bioinformatician, I have two group of sequences (they are nucleotide and in fasta format), each group includes around 40,000 sequences ranging from 100 bp to 12 kb. I want to know how can I align the sequences from a group to the another and find the best pair for each fragment. How can I do that? is there any softwares that can I use? second Q how can I find secondary structures of the sequences in each groups? which program should I use? Thanks MS

[Medhat]

about the alignment part i hope that you can clarify it more

[saeid]

What I want to do is aligning each fragment (sequence) in one group against another group and only find the best pair for that one it continues for all fragments

Answer 1

[Medhat]

this answer about the second part secondary structures this is an online service to do so Mfold The mfold web server is one of the oldest web servers in computational molecular biology. It has been in continuous operation since the fall of 1995 when it was introduced at Washington University's School of Medicine. it is so easy and simple for non bioinformation

about the alignment this is also a simple and powerful yet software MEGA is an integrated tool for conducting sequence alignment MEGA is an integrated tool for conducting sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. MEGA is used by biologists in a large number of laboratories for reconstructing the evolutionary histories of species and inferring the extent and nature of selective forces shaping the evolution of genes and species.

[saeid]

Thank you, do you know I can find miRNA structure as well via this program? also as my file is a big file it is easy to do it online.

[Medhat]

you are most welcome about the size of your file it is not a problem for miRNA you can use this program http://evryrna.ibisc.univ-evry.fr/miRNAFold/