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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 global alignment of two sequences?
Program name: needle
Notes: A global alignment will align two sequences over their entire length. This type of alignment is most appropriate where
two sequences are known to have diverged from a common ancestor.
See also: - If you are trying to create a global alignment of two very long sequences and find that needle is too slow,
there is a more suitable program available called, "stretcher"
[run stretcher /
stretcher manual]
- To create a local alignment, where the best matching segments of the two sequences are aligned, use
"water" [run water /
water manual]
Example output from needle.
#=======================================
# Aligned_sequences: 2
# 1: Q7X170_SERLI
# 2: O30346_9ENTR
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 249
# Identity: 124/249 (49.8%)
# Similarity: 178/249 (71.5%)
# Gaps: 8/249 ( 3.2%)
# Score: 648.5
#=======================================
Q7X170_SERLI 1 MSNFFFNNETINASIKEELERGLSKYNNIKYAYAIMNKRNPASFSIISN- 49
||..|.::|.|:..||:...:.|..|:.:|:::.::||:||:...|||:
O30346_9ENTR 1 MSPLFTDSEIISKVIKKHFTKNLDHYDGVKFSFMVLNKKNPSQMIIISSY 50
Q7X170_SERLI 50 RTEWFEFYIKNNYQFIDPVLITASHRITPFTWDKDLEIGAGLKLPKIFDM 99
..||.:.|.:|.||.||||::.:.::|:||:|:|.|.|...|:|.||||:
O30346_9ENTR 51 PDEWVDLYKENKYQHIDPVVLASFNKISPFSWEKSLVINTRLQLAKIFDL 100
Q7X170_SERLI 100 AKNYNIINGYTFVLHDHHHNLVVLSIMLDKHCDADVEQQIDNNKAEIQML 149
:|.||||||||||||||..||.:|||::|.....|||:.|:..|...|||
O30346_9ENTR 101 SKKYNIINGYTFVLHDHGDNLAMLSIIVDSSYPDDVEKFIEEKKDTFQML 150
Q7X170_SERLI 150 LITMHGKMTTLYQEMSTPADFEKMNQREFFSKRENEIIYWASLGKSYQEI 199
||..:.::.:|.:||.... ::::.::.||:|||||:||||:||:|.|:
O30346_9ENTR 151 LIEAYEEIISLCREMIESK--KQLHNKDIFSQRENEILYWASMGKTYLEV 198
Q7X170_SERLI 200 ALILGIKLTTVKYHIGNAVKKLGVTNAKHAIRLGVELQLIRPLLADTEG 248
|:|||||.:|||:||||.||||||.|||||||||||||||:|:.
O30346_9ENTR 199 AIILGIKTSTVKFHIGNVVKKLGVLNAKHAIRLGVELQLIKPVQ----- 242
Further reading: needle background
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