query sequence is input sequence or its reverse complement

Question

[Hosny.yasmine123]

>sp|O14920.1|IKKB_HUMAN RecName: Full=Inhibitor of nuclear factor kappa-B kinase subunit beta; Short=I-kappa-B-kinase beta; Short=IKK-B; Short=IKK-beta; Short=IkBKB; AltName: Full=I-kappa-B kinase 2; Short=IKK2; AltName: Full=Nuclear factor NF-kappa-B inhibitor kinase beta; Short=NFKBIKB; AltName: Full=Serine/threonine protein kinase IKBKB
MSWSPSLTTQTCGAWEMKERLGTGGFGNVIRWHNQETGEQIAIKQCRQELSPRNRERWCLEIQIMRRLTH
PNVVAARDVPEGMQNLAPNDLPLLAMEYCQGGDLRKYLNQFENCCGLREGAILTLLSDIASALRYLHENR
IIHRDLKPENIVLQQGEQRLIHKIIDLGYAKELDQGSLCTSFVGTLQYLAPELLEQQKYTVTVDYWSFGT
LAFECITGFRPFLPNWQPVQWHSKVRQKSEVDIVVSEDLNGTVKFSSSLPYPNNLNSVLAERLEKWLQLM
LMWHPRQRGTDPTYGPNGCFKALDDILNLKLVHILNMVTGTIHTYPVTEDESLQSLKARIQQDTGIPEED
QELLQEAGLALIPDKPATQCISDGKLNEGHTLDMDLVFLFDNSKITYETQISPRPQPESVSCILQEPKRN
LAFFQLRKVWGQVWHSIQTLKEDCNRLQQGQRAAMMNLLRNNSCLSKMKNSMASMSQQLKAKLDFFKTSI
QIDLEKYSEQTEFGITSDKLLLAWREMEQAVELCGRENEVKLLVERMMALQTDIVDLQRSPMGRKQGGTL
DDLEEQARELYRRLREKPRDQRTEGDSQEMVRLLLQAIQSFEKKVRVIYTQLSKTVVCKQKALELLPKVE
EVVSLMNEDEKTVVRLQEKRQKELWNLLKIACSKVRGPVSGSPDSMNASRLSQPGQLMSQPSTASNSLPE
PAKKSEELVAEAHNLCTLLENAIQDTVREQDQSFTALDWSWLQTEEEEHSCLEQAS

(base) ngs@NU-NGS:~/Downloads$ #! /bin/bash
(base) ngs@NU-NGS:~/Downloads$ vim seq
(base) ngs@NU-NGS:~/Downloads$ bash seq
pos=1
pos=7
(base) ngs@NU-NGS:~/Downloads$ vim q3
(base) ngs@NU-NGS:~/Downloads$ bash q3
q3: line 4: syntax error near unexpected token `|'
q3: line 4: `exist=(echo "$seq" | grep -i "$query")'


#!/bin/bash
seq="$1"
query="$2"exist=(echo "$seq" | grep -i "$query")
revComp=$(echo "$seq" > tr "nacgtNACGT" "ntgcaNTGCA" | rev)
exist_rc=$(echo "$revComp" | grep -i "$query")
if [ "$exist" ] |  [ "$exist_rc" ];then
  echo "query exist"
fi
error in line 4 at exist ...........

how to fix it please???????

[rpolicastro]

What are you trying to do?

[cpad0112]

Are you searching for nucleotide motif in a protein sequence? Your sequence is protein/AA sequence and your search strings are NT motifs.