How to create motifs using biopython when the sequence object contain gaps (-)?
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10 months ago
mrj ▴ 100

I have a gapped candidate promoter sequence for motif predictions. I am expecting to get two motifs, 1) left side motif, 2) right side motif.

For the task, I am using biopython. Following is my code. My code halts because it cannot deal wth - in my dataset (given below).

Could you please help me to resolve this issue?

    for seq_record in SeqIO.parse(each, "fasta"):
        print(seq_record.seq)

        seqList.append(seq_record.seq.upper())
    createdMotif = motifs.create(seqList)

Following is my dataset.

>Patl_2558(bioA) Score=7.6 Pos=-44 [Pseudoalteromonas atlantica T6c]
TTGTCAACT---------------ACTTTACAA
>Patl_2557(bioB) Score=7.6 Pos=-87 [Pseudoalteromonas atlantica T6c]
TTGTAAAGT---------------AGTTGACAA
>MADE_02211(bioB) Score=6.9 Pos=-86 [Alteromonas macleodii 'Deep ecotype']
TgGTAAAgg---------------aGTTgACAA
>MADE_02212(bioA) Score=6.9 Pos=-18 [Alteromonas macleodii 'Deep ecotype']
TTGTcAACt---------------ccTTTACcA
>GHTCC_010100004703(bioA) Score=8.7 Pos=-44 [Glaciecola sp. HTCC2999]
TTGTCAACC---------------AGTTTACAA
>GHTCC_010100004698(bioB) Score=8.7 Pos=-92 [Glaciecola sp. HTCC2999]
TTGTAAACT---------------GGTTGACAA
>CPS_2593(bioA) Score=7.7 Pos=-33 [Colwellia psychrerythraea 34H]
ATGTCAACG---------------GGTTAACAA
>CPS_2594(bioB) Score=7.7 Pos=-87 [Colwellia psychrerythraea 34H]
TTGTTAACC---------------CGTTGACAT
>ATW7_13078(bioA) Score=8 Pos=-34 [Alteromonadales bacterium TW-7]
TTGTCAACG---------------AGTTTACAT
>ATW7_13073(bioB) Score=8 Pos=-95 [Alteromonadales bacterium TW-7]
ATGTAAACT---------------CGTTGACAA
>PSHAa1609(bioB) Score=8 Pos=-99 [Pseudoalteromonas haloplanktis TAC125]
ATGTAAACT---------------CGTTGACAA
>PTD2_19562(bioA) Score=7.9 Pos=-34 [Pseudoalteromonas tunicata D2]
TTGTCAACA---------------AGTTTACAT
>PTD2_19567(bioB) Score=7.9 Pos=-95 [Pseudoalteromonas tunicata D2]
ATGTAAACT---------------TGTTGACAA
>OS145_05987(bioA) Score=6.8 Pos=-44 [Idiomarina baltica OS145]
CTGTCAATT---------------ACTTTACAA
>OS145_05992(bioB) Score=6.8 Pos=-95 [Idiomarina baltica OS145]
TTGTAAAGT---------------AATTGACAG
>IL1324(bioB) Score=6.6 Pos=-89 [Idiomarina loihiensis L2TR]
TTGTAAAgt---------------taTTgACAg
>IL1325(bioA) Score=6.6 Pos=-45 [Idiomarina loihiensis L2TR]
cTGTcAAta---------------acTTTACAA
alphabet gaps motifs_create biopython • 266 views
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