Author: bugman
Date: Thu Jan 22 15:53:43 2015
New Revision: 27264
URL: http://svn.gna.org/viewcvs/relax?rev=27264&view=rev
Log:
Updated the gap penalties in the Test_align_protein.test_align_pairwise unit
test.
This is from the unit test module _lib._sequence_alignment.test_align_protein.
Modified:
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
Modified:
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py?rev=27264&r1=27263&r2=27264&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
(original)
+++ trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
Thu Jan 22 15:53:43 2015
@@ -38,13 +38,13 @@
- 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
-
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.
- From online servers, the results should be::
-
+ From online servers, the results with a gap open penalty of 5 and gap
extend of 1 should be::
+
https://www.ebi.ac.uk/Tools/psa/emboss_needle/
EMBOSS_001
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA
- :|||:|||:|||:|| | | ||||||||||:|..
.|:|:||||||||:||:.|::|.:|:|.||
+ :|||:|||:|||:|| | | ||||||||||:|..
.|:|:||||||||:||:.|::|.:|:|.||
EMBOSS_001
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-
-
+
http://web.expasy.org/cgi-bin/sim/sim.pl?prot
UserSeq1
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKL
UserSeq2
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
@@ -57,8 +57,8 @@
print(seq1)
print(seq2)
- # Perform the alignment.
- align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62',
gap_penalty=10.0)
+ # Perform the alignment.
+ align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62',
gap_open_penalty=5.0, gap_extend_penalty=1.0)
print(align1)
print(align2)
print(gaps)
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