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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 prepare a sequence figure for publication?
Program name: showseq
Notes: Nucleotide sequences can be prepared for publication by displaying translated regions (any combination of frames),
any or all restriction sites and any annotation in context. In addition, regions of both nucleotide and protein sequences
can be highlighted using uppercase letters or by displaying with colours (when the output is formated as html). Features derived from
EMBL or UniProt-SwissProt entries can also be displayed.
Figure 1, Example output from showseq - used to illustrate an annotation, translation of a defined region,
uppercase highlighting of a defined region and a restriction enzyme site.
M T S S L L L A F L L L A P T T V A T P R
cccagcaATGACCTCCTCATTGCTTCTGGCCTTTCTCCTCCTGGCTCCAACCACAGTGGCCACTCCCAGA
----:----|----:----|----:----|----:----|----:----|----:----|----:----|
10 20 30 40 50 60 70
|----------------------------------------------------|
sig peptide
A G G Q C P A C G G P T L E L E S Q R E L L L D
GCTGGCGGTCAGTGTCCAGCATGTGGGGGGCCCACCTTGGAACTGGAGAGCCAGCGGGAGCTGCTTCTTG
----:----|----:----|----:----|----:----|----:----|----:----|----:----|
80 90 100 110 120 130 140
EcoRI
\
L A K R S I L D *
ATCTGGCCAAGAGAAGCATCTTGGACTAGctgcacctcacccagcgctgaattctgaaccgccctgtgtc
----:----|----:----|----:----|----:----|----:----|----:----|----:----|
150 160 170 180 190 200 210
Figure 2, Example output from showseq - using the pre-defined display format: "Baroque"
P S N D L L I A S G L S P P G S N H S G
P A M T S S L L L A F L L L A P T T V A
Q Q * P P H C F W P F S S W L Q P Q W P
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
CspCI
BsrDI | CjeI Tsp4CI
| BsrDI | |BssKI | CfrI
| | MnlI | |EcoRII | AceIII
| | | MnlI | || AeuI | | BalI
| | | |BseRI | || ScrFI | | HaeI
| | | || HaeI | || | CviJI | | CviJI
BseYI | | | || CviJI | || | |NlaIV | | HaeIII
| BseRI | | | || HaeIII | || | || MnlI | | |TspRI
\ \ \ \
CCCAGCAATGACCTCCTCATTGCTTCTGGCCTTTCTCCTCCTGGCTCCAACCACAGTGGC
----:----|----:----|----:----|----:----|----:----|----:----|
GGGTCGTTACTGGAGGAGTAACGAAGACCGGAAAGAGGAGGACCGAGGTTGGTGTCACCG
/ / / / / / / / / / /// / / /
| | | BsrDI | | | | CspCI | ||MnlI | | HaeIII
| | BsrDI | | | CjeI | |NlaIV | | CviJI
| BseYI | | HaeIII | EcoRII | | HaeI
BseRI | | CviJI | CviJI | | BalI
| | HaeI | BssKI | Tsp4CI
| BseRI ScrFI TspRI
| MnlI AeuI
MnlI
----:----|----:----|----:----|----:----|----:----|----:----|
G L L S R R M A E P R E G G P E L W L P
X W C H G G * Q K Q G K E E Q S W G C H
G A I V E E N S R A K R R R A G V V T A
Further reading: showseq background
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