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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 multiple sequence alignment?
Program name: emma
Notes: The program, emma uses clustalW to create a multiple sequence alignment of protein or nucleotide sequences.
There are two methods of alignment available: slow-accurate and fast-but-less-accurate. The slow-accurate method
can be used for short sequences (e.g. less than 1000 residues) but will be VERY SLOW if the sequences are long or if
there are a lot of sequences to be aligned (e.g. more than 100).
Example multiple sequence alignment produced using emma
O30346_9ENTR ---------MSPLFTDSEIISKVIKKHFTKNLDHYDGVKFSFMVLNKKNP
EXPR_ERWCH ---------MSISFSNVDFINSTIQSYLNRKLKSYGDPKYAYLIMNKKKP
Q7X170_SERLI ---------MSNFFFNNETINASIKEELERGLSKYNNIKYAYAIMNKRNP
CAG28516 MYKLHVLDGELDNLIDALELARDQRMIKQALRHFCESNGFDRFAHLNVRS
O30346_9ENTR SQMIIISSYPDEWVDLYKENKYQHIDPVVLASFNKISPFSWEKSLVINTR
EXPR_ERWCH TDVVIISNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSK
Q7X170_SERLI ASFSIISNR-TEWFEFYIKNNYQFIDPVLITASHRITPFTWDKDLEIGAG
CAG28516 TETCVLTTYPAEWQRLYFDKKYALIDPVVISAKRNMEIFSWSQDDASKYS
O30346_9ENTR LQLAKIFDLSKKYNIINGYTFVLHDHGDNLAMLSIIVDSSYPDDVEKFIE
EXPR_ERWCH LKFSRIFNLSKDYDIVNGYTFVLHSPGNNLAALSFMIEEHRSEELEEIIQ
Q7X170_SERLI LKLPKIFDMAKNYNIINGYTFVLHDHHHNLVVLSIMLDKHCDADVEQQID
CAG28516 KDVKRFFREADDFGIRSGLSIPIRTPFGGTAILTLASEQRR---------
O30346_9ENTR EKKDTFQMLLIEAYEEIISLCREMIESKK--QLHNKDIFSQRENEILYWA
EXPR_ERWCH NNKDKLQMLLISAHEKLTSLYREMSRNRNNSKSQEADLFSQRENEILHWA
Q7X170_SERLI NNKAEIQMLLITMHGKMTTLYQEMSTPADFEKMNQREFFSKRENEIIYWA
CAG28516 -VDFAGIQDTVRAMNAVAFAHAHLNRVAAAPCRRTKYELTPREVTCLTWA
O30346_9ENTR SMGKTYLEVAIILGIKTSTVKFHIGNVVKKLGVLNAKHAIRLGVELQLIK
EXPR_ERWCH SMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVEMNLIK
Q7X170_SERLI SLGKSYQEIALILGIKLTTVKYHIGNAVKKLGVTNAKHAIRLGVELQLIR
CAG28516 SLGKTMSEIADLLQIDVRTVRNYLDLAREKLGGSNIAHAVRLAVMQHLI-
O30346_9ENTR PVQ------
EXPR_ERWCH PVGPAKARS
Q7X170_SERLI PLLADTEG-
CAG28516 ---------
Further reading: emma background
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