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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.
Can I improve the appearance of an alignment?
Program name: showalign
Notes: Showalign can be used to highlight identities, similarities or defined regions of a pre-existing alignment.
Example output from showalign (show: "all of the sequences")
Q5R4K2 FSnPWCYENFIQARSLRRAQDIRKQMLgIMDRHKLDVVScGKStvRVQKAIcSGFFrNaA
Q86YB2 FSnPWCYENFIKARSLRRAQDIRKQMLgIMDRHKLDVVScGKStvRVQKAIcSGFFrNaA
NP_659080 FSnPWCYENFIQARSLRRAQDIRKQMLgIMDRHKLDVVScGKStvRVQKAIcSGFFrNaA
Q56WL7 FSgPWCFENFIQSRSLRRAQDVRKQLLsIMDKYKLDVVTaGKNftKIRKAItAGFFfHgA
Example output from showalign (show: "non-identities between the sequences")
Consensus FSxPWCYENFIQARSLRRAQDIRKQMLxIMDRHKLDVVSxGKSxxRVQKAIxSGFFxNxA
Q5R4K2 ..N........................G...........C...TV......C....R.A.
Q86YB2 ..N........k...............G...........C...TV......C....R.A.
NP_659080 ..N........................G...........C...TV......C....R.A.
Q56WL7 ..G...f.....s........v...l.S...ky.....tA..nFTkir...Ta...FhG.
Consensus FSxPWCYENFIQARSLRRAQDIRKQMLxIMDRHKLDVVSxGKSxxRVQKAIxSGFFxNxA
Example output from showalign (show: "similarities between the sequences")
1090 1100 1110 1120 1130 1140
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus FSxPWCYENFIQARSLRRAQDIRKQMLxIMDRHKLDVVSxGKSxxRVQKAIxSGFFxNxA
Q5R4K2 FS.PWCYENFIQARSLRRAQDIRKQML.IMDRHKLDVVS.GKS..RVQKAI.SGFF.N.A
Q86YB2 FS.PWCYENFIkARSLRRAQDIRKQML.IMDRHKLDVVS.GKS..RVQKAI.SGFF.N.A
NP_659080 FS.PWCYENFIQARSLRRAQDIRKQML.IMDRHKLDVVS.GKS..RVQKAI.SGFF.N.A
Q56WL7 FS.PWCfENFIQsRSLRRAQDvRKQlL.IMDkyKLDVVt.GKn..kirKAI.aGFF.h.A
Consensus FSxPWCYENFIQARSLRRAQDIRKQMLxIMDRHKLDVVSxGKSxxRVQKAIxSGFFxNxA
Further reading: showalign background
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