A sequence is break to form new sequence

Question

[waqasnayab]

Hi Community,

I have two fasta files: 1. right.fasta: head

>COSN17913384
CAAGAGGGGTGAATGTGTTTTGCATGCACAAGGGACAGGAG
>COSN6473262
TCAGAGCTGGTGGGGTGGAGGGACAGAAACAAGTGGGAGAA
>COSN17979053
TATACCTACCTTATAGATAAAGAAATTGAAGCTTATAGAGT
>COSN15187127
TTTTTCCTTATGATACTCTACTGCCTCTCCATGGATAAAGA
>COSN17118087
AACTCCTGACCTCAGGTGATACACCTGCCTCGGCCTCCCAA

tail:

>COSN18618110
CTATGCCAGGACAGTGTAGCAGCCCCGTGGTGCTGACAAAT
>COSN18201496|COSN18701930|COSN18583086
CAGCAGCTATAGGTCTGGGGCGGGGCCGCTTGGCAAGAACA
>COSN18653667
AAGTCATTGCTGTCCTGTCCCGCCTGGGGCTTTTGTGGACC
>COSN18329724
GTGAGGTGCCTGGTCTGAGAGGGCCTTGACCATTCCCCTTG

1. wrong.fasta: head >COSN17913384 CAAGAGGGGTGAATGTGTTTCGCATGCACAAGGGACAGGAG >COSN6473262 TCAGAGCTGGTGGGGTGGAGAGACAGAAACAAGTGGGAGAA >COSN17979053 TATACCTACCTTATAGATAAGGAAATTGAAGCTTATAGAGT >COSN15187127 TTTTTCCTTATGATACTCTATTGCCTCTCCATGGATAAAGA >COSN17118087 AACTCCTGACCTCAGGTGATCCACCTGCCTCGGCCTCCCAA tail: >COSN8613750|COSN18681804|COSN18352203|COSN5269362 GTGAGCATGGAGGGCCATGCACACCTGGACAGGGATGAGGG >COSN18636019 CTATGCCAGGACAGTGTAGCTGCCCCGTGGTGCTGACAAAT >COSN18618110 CAGCAGCTATAGGTCTGGGGTGGAGCCGCTTGGCAAGAACA >COSN18201496|COSN18701930|COSN18583086 AAGTCATTGCTGTCCTGTCCTGCCTGGGGCTTTTGTGGACC >COSN18653667 GTGAGGTGCCTGGTCTGAGATGGCCTTGACCATTCCCCTTG

As you can see in right.fasta, >COSN18329724 is the last header with its sequence, GTGAGG .... CCTTG but in wrong.fasta the sequence is the same but with wrong header. Infact in wrong.fasta, the header comes down a sequence. So, I investigated that what happens in wrong.fasta: grep -A 7 -B 4 COSN229024 right.fasta

COSN9627597 CGCTGGGCTCGCCTCCAGCCAGGCCTGCATTCCCAAATCTA COSN8175610 CAAGAGAGAAATTCTGACACTTCCTAAGTCTACCAAGCTTT COSN229024 CACTATAAAAATATTAAGAGAATGTCCTAATGAAGTGTGCA COSN18183003 CTGTACCTTGGAAATGTCTGCTGTTCGTAACTTCTTCAGTT COSN18487588 ATGCCTAGTTCTAATCATCTCATCCTGTGTTTGTGATTGAT COSN1681903|COSN1178783 TGCTTACCCCTTAAATGCAATTTATTTACTTTTACCACTGT

grep -A 7 -B 4 COSN229024 wrong.fasta

COSN9627597 CGCTGGGCTCGCCTCCAGCCTGGCCTGCATTCCCAAATCTA COSN8175610 CAAGAGAGAAATTCTGACACCTCCTAAGTCTACCAAGCTTT COSN229024 CACTATAAAAATATTAAGAGA COSN18183003 TGTGTTTGTGATTGATGT COSN18487588 TGCTTACCCCTTAAATGCAACTTATTTACTTTTACCACTGT COSN1681903|COSN1178783 CTTCCCAACTCATGAGTTCTGAATTCCAATACGTCTCCATT

I observed that in wrong.fasta approximately half of the sequence of >COSN229024 breaks up and forms a new sequence >COSN18183003. In the end, the whole order mess up after breakup. So, I want to put the break part of >COSN229024 back into the >COSN229024 in wrong.fasta.

I checked the both fasta files and I am sure this in the only problem. My desired output would be the same if I:

grep -A 7 -B 4 COSN229024 wrong.fasta

COSN9627597 CGCTGGGCTCGCCTCCAGCCAGGCCTGCATTCCCAAATCTA COSN8175610 CAAGAGAGAAATTCTGACACTTCCTAAGTCTACCAAGCTTT COSN229024 CACTATAAAAATATTAAGAGAATGTCCTAATGAAGTGTGCA COSN18183003 CTGTACCTTGGAAATGTCTGCTGTTCGTAACTTCTTCAGTT COSN18487588 ATGCCTAGTTCTAATCATCTCATCCTGTGTTTGTGATTGAT COSN1681903|COSN1178783 TGCTTACCCCTTAAATGCAATTTATTTACTTTTACCACTGT

Any help appreciated,

Thanks,

Waqas.

[GenoMax]

Instead of using "Block quotes" button use the "code" (101010 button) to format these sequences. It makes it very hard to read these the way they are now. I will fix one block for you as an example.

[waqasnayab]

Hi Community,

I have two fasta files: 1. head right.fasta:

>COSN17913384
CAAGAGGGGTGAATGTGTTTTGCATGCACAAGGGACAGGAG
>COSN6473262
TCAGAGCTGGTGGGGTGGAGGGACAGAAACAAGTGGGAGAA
>COSN17979053
TATACCTACCTTATAGATAAAGAAATTGAAGCTTATAGAGT
>COSN15187127
TTTTTCCTTATGATACTCTACTGCCTCTCCATGGATAAAGA
>COSN17118087
AACTCCTGACCTCAGGTGATACACCTGCCTCGGCCTCCCAA

tail:

>COSN18618110
CTATGCCAGGACAGTGTAGCAGCCCCGTGGTGCTGACAAAT
>COSN18201496|COSN18701930|COSN18583086
CAGCAGCTATAGGTCTGGGGCGGGGCCGCTTGGCAAGAACA
>COSN18653667
AAGTCATTGCTGTCCTGTCCCGCCTGGGGCTTTTGTGGACC
>COSN18329724
GTGAGGTGCCTGGTCTGAGAGGGCCTTGACCATTCCCCTTG

1. head wrong.fasta:

   COSN17913384 CAAGAGGGGTGAATGTGTTTCGCATGCACAAGGGACAGGAG COSN6473262 TCAGAGCTGGTGGGGTGGAGAGACAGAAACAAGTGGGAGAA COSN17979053 TATACCTACCTTATAGATAAGGAAATTGAAGCTTATAGAGT COSN15187127 TTTTTCCTTATGATACTCTATTGCCTCTCCATGGATAAAGA COSN17118087 AACTCCTGACCTCAGGTGATCCACCTGCCTCGGCCTCCCAA

tail:

>COSN8613750|COSN18681804|COSN18352203|COSN5269362
GTGAGCATGGAGGGCCATGCACACCTGGACAGGGATGAGGG
>COSN18636019
CTATGCCAGGACAGTGTAGCTGCCCCGTGGTGCTGACAAAT
>COSN18618110
CAGCAGCTATAGGTCTGGGGTGGAGCCGCTTGGCAAGAACA
>COSN18201496|COSN18701930|COSN18583086
AAGTCATTGCTGTCCTGTCCTGCCTGGGGCTTTTGTGGACC
>COSN18653667
GTGAGGTGCCTGGTCTGAGATGGCCTTGACCATTCCCCTTG

As you can see in right.fasta, >COSN18329724 is the last header with its sequence, GTGAGG .... CCTTG but in wrong.fasta the sequence is the same but with wrong header. Infact in wrong.fasta, the header comes down a sequence. So, I investigated that what happens in wrong.fasta:

grep -A 7 -B 4 COSN229024 right.fasta

>COSN9627597
CGCTGGGCTCGCCTCCAGCCAGGCCTGCATTCCCAAATCTA
>COSN8175610
CAAGAGAGAAATTCTGACACTTCCTAAGTCTACCAAGCTTT
>COSN229024
CACTATAAAAATATTAAGAGAATGTCCTAATGAAGTGTGCA
>COSN18183003
CTGTACCTTGGAAATGTCTGCTGTTCGTAACTTCTTCAGTT
>COSN18487588
ATGCCTAGTTCTAATCATCTCATCCTGTGTTTGTGATTGAT
>COSN1681903|COSN1178783
TGCTTACCCCTTAAATGCAATTTATTTACTTTTACCACTGT

grep -A 7 -B 4 COSN229024 wrong.fasta:

>COSN9627597
CGCTGGGCTCGCCTCCAGCCTGGCCTGCATTCCCAAATCTA
>COSN8175610
CAAGAGAGAAATTCTGACACCTCCTAAGTCTACCAAGCTTT
>COSN229024
CACTATAAAAATATTAAGAGA
>COSN18183003
TGTGTTTGTGATTGATGT
>COSN18487588
TGCTTACCCCTTAAATGCAACTTATTTACTTTTACCACTGT
>COSN1681903|COSN1178783
CTTCCCAACTCATGAGTTCTGAATTCCAATACGTCTCCATT

I observed that in wrong.fasta approximately half of the sequence of >COSN229024 breaks up and forms a new sequence >COSN18183003. In the end, the whole order mess up after breakup. So, I want to put the break part of >COSN229024 back into the >COSN229024 in wrong.fasta.

I checked the both fasta files and I am sure this in the only problem. My desired output would be the same if I: grep -A 7 -B 4 COSN229024 wrong.fasta

>COSN9627597
CGCTGGGCTCGCCTCCAGCCTGGCCTGCATTCCCAAATCTA
>COSN8175610
CAAGAGAGAAATTCTGACACCTCCTAAGTCTACCAAGCTTT
>COSN229024
CACTATAAAAATATTAAGAGATGTGTTTGTGATTGATGT
>COSN18183003
TGCTTACCCCTTAAATGCAACTTATTTACTTTTACCACTGT
>COSN18487588
CTTCCCAACTCATGAGTTCTGAATTCCAATACGTCTCCATT

Any help appreciated,

Thanks,

Waqas.

[WouterDeCoster]

I would be more worried by how your error originated.