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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 do I translate a nucleotide sequence?
Program name: transeq
Notes: Translate a sequence in any of the 3 forward or three reverse sense frames, in all three forward or
reverse frames, or in all six frames.
Example output from transeq using the EMBL database entry, D84467 (translating between nucs, 105-1196)
>D84467_1 Rhodopseudomonas palustris recA gene for RecA protein
MAAPTALRIVEGSSMDKSKALSAALSQIERQFGKGSVMKLGKNDRAMEIETISSGSLGLD
IALGVGGLPKGRIVEIYGPESSGKTTLALHCVAEAQKKGGICAFIDAEHALDPVYARKLG
VNVDDLLISQPDHGEQALEIADTLVRSGAIDVLIVDSVAALVPRAELEGEMGDALPGLQA
RLMSQALRKLTASINKSNTMVIFINQIRMKIGVMYGSPETTTGGNALKFYASVRLDIRRI
GAIKERDEVIGNQTRVKVVKNKLAPPFKQVEFDIMYGEGVSKMGEILDLGVKAGIVEKSG
AWFSYDSQRLGQGRENAKSFLRSNPDMTAKIEAAIRQNSGLIAEQILAGSPERDADGEEP
IEE*
>D84467_2 Rhodopseudomonas palustris recA gene for RecA protein
WLPPPHCVSSKVLPWTNPRRSPPRCPRSNVSSVRAR**SSARTTARWKSRRFPPGRSGST
SRSASAACRRAGSSKFTGRNRRARPRWRCIASPRPRRRAASAPSSTPNTRSTRSMPASSA
SMSTTC*SRSPTMASRRWKSPTRWCAPARSTC*SSTRWRRWCRAPNSKAKWATRCRACRP
A**ARRCAS*PRRSTSPTPW*SSSTRSG*RSA*CMARRKPPPAATR*SSTPRSVSTSAAS
ARSRSATR*SATRPASRW*RTSWRRRSSRSNSTSCTARASPRWARSSTSASRPASSRSPA
PGSPMTASGSARDARTPSRSCAPTRT*PPRSKRRSARTPA*SPNKSSPARRSATPTAKSR
SRN
>D84467_3 Rhodopseudomonas palustris recA gene for RecA protein
GCPHRIAYRRRFFHGQIQGALRRAVPDRTSVR*GLGDEARQERPRDGNRDDFLRVARARH
RARRRRPAEGPDRRNLRAGIVGQDHAGAALRRRGPEEGRHLRLHRRRTRARPGLCPQARR
QCRRPADLAARPWRAGAGNRRHAGALRRDRRADRRLGGGAGAARRTRRRNGRRAAGPAGP
PDEPGAAQADRVDQQVQHHGDLHQPDPDEDRRDVWLAGNHHRRQRAEVLRLGPSRHPPHR
RDQGARRGDRQPDPRQGGEEQVGAAVQAGRIRHHVRRGRLQDGRDPRPRRQGRHRREVRR
LVLL*QPAARPGTRERQVVPALQPGHDRQDRSGDPPELRPDRRTNPRRLAGARRRRRRAD
RGI
>D84467_4 Rhodopseudomonas palustris recA gene for RecA protein
LFLDRLFAVGVALRRAGEDLFGDQAGVLADRRFDLGGHVRVGAQERLGVLASLAEPLAVI
GEPGAGLLDDAGLDAEVEDLAHLGDALAVHDVEFDLLERRRQLVLHHLDAGLVADHLVAL
LDRADAADVETDRGVELQRVAAGGGFRRAIHHADLHPDLVDEDHHGVGLVDRRGQLAQRL
AHQAGLQARQRVAHFAFEFGARHQRRHRVDDQHVDRAGAHQRVGDFQRLLAMVGLRDQQV
VDIDAELAGIDRVERVFGVDEGADAALLLGLGDAMQRQRGLARRFRPVNFDDPALRQAAD
AERDVEPERPGGNRLDFHRAVVLAELHHRALTELTFDLGQRGGERLGFVHGRTFDDTQCG
GGSH
>D84467_5 Rhodopseudomonas palustris recA gene for RecA protein
IPRSALRRRRRAPASRRGFVRRSGRSSGGSPLRSWRSCPGWSAGTTWRSRVPGRAAGCHR
RTRRRTSRRCRP*RRGRGSRPSWRRPRRT*CRIRPA*TAAPTCSSPP*RGSGCRSPRRAP
*SRRCGGCRDGPRRRTSARCRRWWFPASHTSRRSSSGSG**RSPWCWTC*STRSACAAPG
SSGGPAGPAARRPFRLRVRRAAPAPPPSRRSARRSRRSAPACRRFPAPARHGRAARSAGR
RH*RRACGHRPGRARVRRR*RRRCRPSSGPRRRNAAPAWSCPTIPARKFRRSGPSAGRRR
RARCRARATRRKSSRFPSRGRSCRASSPSPYRTDVRSGTARRRAPWICPWKNLRRYAMRW
GQPX
>D84467_6 Rhodopseudomonas palustris recA gene for RecA protein
YSSIGSSPSASRSGEPARICSAIRPEFWRIAASILAVMSGLERRNDLAFSRPWPSRWLS*
ENQAPDFSTMPALTPRSRISPILETPSPYMMSNSTCLNGGANLFFTTLTRVWLPITSSRS
LIAPMRRMSRRTEA*NFSALPPVVVSGEPYITPIFIRIWLMKITMVLDLLIDAVSLRSAW
LIRRACRPGSASPISPSSSARGTSAATESTISTSIAPERTSVSAISSACSPWSGCEISRS
STLTPSLRA*TGSSACSASMKAQMPPFFWASATQCSASVVLPDDSGP*ISTIRPFGRPPT
PSAMSSPSDPEEIVSISIARSFLPSFITEPLPN*RSIWDSAAESALDLSMEEPSTIRNAV
GAAX
Further reading: transeq background
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