Entering edit mode
3.0 years ago
yarongeffen
•
0
Hi all,
in continuation to the following post: skip redundant vs needle
I used needle command with the following sequences:
>1
MMMMMMMFKL
>2
MMMMMMMVYA
and got these results:
# Identity: 6/11 (54.5%)
# Similarity: 8/11 (72.7%)
# Gaps: 2/11 (18.2%)
In addition, when I used skipredundant command with threshold 75.0, the output file was:
>1
MMMMMMMFKL
As you can see the similarity between the sequences is 72.7%, so both had to appear in the output file.
Why does only the first sequence appear in the output file?
Thanks
You are comparing two programs that are doing different things.
needle
is a global aligner so it is going to look at the entire length of sequences and produce a result.With
skipredundant
you are trying to come up with a redundant dataset. Mode 1 (LINK for manual)One of these conditions is being satisfied.
Beyond this you will need to examine the actual code to see what exactly may be going on with these two tools.
This description is from the needle manual (LINK):
As I understand, skipredundant uses the same technique as needle, doesn't it?
Furthermore, how can I take a look at the code?
It is using the same implementation of
needle
but which parameters it is using is what you may need to find in the source code. You can download the code for EMBOSS here.Have you tried to compare these results with larger/real data sets? That may clarify things further.