Supermatcher

[Shibl Mourad]

RE: Instalation and D'd problem.Hi all,

I am using supermatcher to align 2 sequences, and it seems that the order of the sequences affects the results dramatically  (see example below).

Is that normal?

Shibl

Note:  The following examples where build by downloading AP000926.5 and AP001970.3 from entrez and then calling
supermatcher with wordlen=20, all other parameters are kept as default.

########################################
# Program:  supermatcher
# Rundate:  Wed Jul 31 11:54:34 2002
# Report_file: ap000926.supermatcher
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: AP000926.5
# 2: AP001970.3
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 57265
# Identity:   40361/57265 (70.5%)
# Similarity: 40361/57265 (70.5%)
# Gaps:       11627/57265 (20.3%)
# Score: 133850.5
# 
#
#=======================================


########################################
# Program:  supermatcher
# Rundate:  Wed Jul 31 11:55:10 2002
# Report_file: ap001970.supermatcher
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: AP001970.3
# 2: AP000926.5
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 52182
# Identity:   50101/52182 (96.0%)
# Similarity: 50101/52182 (96.0%)
# Gaps:        1463/52182 ( 2.8%)
# Score: 242805.0
# 
#
#=======================================

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