local aligment and global alignment

[huda]

hi,
how I can know that a sequence has local similarity or global similarity if this seq. very long?


Also,how I can know what I have to use with my problem multiple or pairwise seq. alignment?

thanks in advance

[mfursov]

Hi
if your sequence is very long try to analyze and view it with tools like dotplot.
Here is an example : [Only registered users see links. ]

With dot-plot you can find high similarity regions, copy regions sequences and analyze them with local alignment tools

[huda]

i,
thanks, really I were waiting who can answer.
please ,can you give link to download dotplot?

Also, you said that I can find high similarity regions using dotplot, then use local alignment.

finding local similarity can be found using algorithm of local align.
Right? why use dotplot to find these similarities ?

maybe you mean, may find local similarity or global similarity using dotplot. Right?

MANY MANY THANKS

[mfursov]

Hi! Here is the link for the tool: [Only registered users see links. ]
Use "tools -> build dotplot" menu to start with it

Dotplot sometimes can be a better tool than BLAST. For example, if you have very long sequences as you said there could be internal restructuring and dotplot will show you the changes while BLAST will not.

[huda]

Originally Posted by mfursov

Hi! Here is the link for the tool: [Only registered users see links. ]
Use "tools -> build dotplot" menu to start with it

Dotplot sometimes can be a better tool than BLAST. For example, if you have very long sequences as you said there could be internal restructuring and dotplot will show you the changes while BLAST will not.

thanks,
i downloded the software, but it need file with .fa format
how get it?
And if my data is not iological, can be in .fa format?

thanks in advance

[huda]

thanks,
I downloded it.
But,it is just accept the 4 alphabets of DNA . My sequences are protein sequences, i.e not just 4 alphabets.
in other hand , I want to know :
does I compare any two sequences that I want to alignment it. If so , what if I have huge number of sequences?.
thanks

[mfursov]

Hi
protein and even raw-text dot-plots support added to UGENE 1.10. Now you can use it even to compare you programming language source files

about huge number of sequences:

1) open them all as a single sequence (use merge option). The regions for original sequences will be highlighted with annotations.

2) Run dot-plot for this merged sequence and see the matches.

If you can describe the algorithm to use to filter the results, there will be possible to use UGENE Workflow Designer as a runner for the batch job to produce only filtered results.

[paddysmith]

What is the main different local aligment and global alignment????????

[newtobioinformatics]

Hi

Global alignment takes entire length of sequence into account while comparing sequences whereas local alignment searches for the region of interest within long sequence. These regions of interest may be divergent.

[FELITSA]

hi,

is the score of local alignment be negative?

thanks