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Bioinformatics FAQ
There are a large number of bioinformatics programs available to CBRG account holders via this web site. These
examples (Frequently Asked Questions) are used to illustrate the use of these tools
in answering typical queries posed by researchers.
The major web-based tools from the CBRG are listed, here.
How can I create a local alignment of two sequences?
Program name: water
Notes: A local alignment will identify the small parts of two sequences where there is some similarity - it does not
assume that the two sequences are similar over their whole length.
See also: To create a global alignment, where the two sequences are aligned over their entire lengths, use
"needle" [run needle /
needle manual]
Example output from water - aligning NM_026472 with a section of mouse chromosome 1.
#=======================================
# Aligned_sequences: 2
# 1: NM_026472_frag
# 2: 1
# Matrix: EDNAFULL
# Gap_penalty: 100.0
# Extend_penalty: 0.5
#
# Length: 101
# Identity: 101/101 (100.0%)
# Similarity: 101/101 (100.0%)
# Gaps: 0/101 ( 0.0%)
# Score: 505.0
#
#
#=======================================
NM_026472_frag 10 caggttttacctgaccaaaaagaagggctttcgggtgaacctaggagaaa 59
||||||||||||||||||||||||||||||||||||||||||||||||||
1 10465 CAGGTTTTACCTGACCAAAAAGAAGGGCTTTCGGGTGAACCTAGGAGAAA 10514
NM_026472_frag 60 ggagaagatgatgaaagaggacatttccaataacattcctaagaagcgta 109
||||||||||||||||||||||||||||||||||||||||||||||||||
1 10515 GGAGAAGATGATGAAAGAGGACATTTCCAATAACATTCCTAAGAAGCGTA 10564
NM_026472_frag 110 a 110
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1 10565 A 10565
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