Question: alignments of DNA sequences
0
gravatar for midox
3.7 years ago by
midox220
Tunisia
midox220 wrote:

Hello,
I have a long sequences file and another small sequences. I want to do an alignment (multiple or global) of small sequences on long sequences.
Do you suggest me the right software? of course I have two files, I do not know if we can make an alignment by taking two fihciers entered into.
thanks for your answers

ADD COMMENTlink modified 3.7 years ago by piet1.7k • written 3.7 years ago by midox220
1
gravatar for stolarek.ir
3.7 years ago by
stolarek.ir580
Poland
stolarek.ir580 wrote:

EMBOSS
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

ADD COMMENTlink written 3.7 years ago by stolarek.ir580

is it the only one that accepts two files?

ADD REPLYlink written 3.7 years ago by midox220
1
gravatar for piet
3.7 years ago by
piet1.7k
planet earth
piet1.7k wrote:
> but the alignment tools do not accept two input file.

Adding more sequences to an already existing multi sequence alignment is often called 'profile aligning'. 'mafft' has three options for this purpose (--add, --addfragments, --addfull). Please read the mafft manual http://mafft.cbrc.jp/alignment/software/addsequences.html

 

ADD COMMENTlink written 3.7 years ago by piet1.7k

thankyou for your help.
But mafft can't do this.
it uses sequences already aligned then added other sequences.
In my case, I want to align a séqences a file with all sequences of another file (not aligned).

ADD REPLYlink written 3.7 years ago by midox220
0
gravatar for bshifaw
3.7 years ago by
bshifaw50
United States
bshifaw50 wrote:

You can try blast 2 to perform the alignment (click here). You'll be able to align sequences from one file with sequences of another. 

ADD COMMENTlink written 3.7 years ago by bshifaw50
0
gravatar for midox
3.7 years ago by
midox220
Tunisia
midox220 wrote:

here is my problem:
I have a file A of sequences DNA and a file B of sequence DNA.
I want to do a multiple sequence alignment of each sequence in file A with all sequences of B.
The problem is I have two files and according to my research there are no multiple alignment tools that accepts two files.

can you help me

ADD COMMENTlink written 3.7 years ago by midox220

Why not just merge the 2 files together and do your alignment? Why would you want to individually align sequences from A with everything from B? If that is really your goal, then you need to create multiple alignment files all consisting of B sequences and a unique A sequence. a script could do this easily, what do the headers look like?

ADD REPLYlink written 3.7 years ago by Adrian Pelin2.3k
0
gravatar for harold.smith.tarheel
3.7 years ago by
United States
harold.smith.tarheel4.4k wrote:

If the number of of long sequences in the file is not too large, then you can format it as FASTA (if it isn't already) and use it as the reference to align the file of short sequences with any of the short read aligners.

ADD COMMENTlink written 3.7 years ago by harold.smith.tarheel4.4k

but the alignment tools do not accept two input file.
they only accept one file. As muscle or mafft.

ADD REPLYlink written 3.7 years ago by midox220
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