Question: adding sequence in ncbi downloaded blast result txt file
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gravatar for Shahzad
4.2 years ago by
Shahzad10
Pakistan
Shahzad10 wrote:

Hello

I am having problem in inserting a sequence in txt file download after blast. NCBI genome workbench does not accept it and says input sequence is not in fasta format. Even after converting this sequence from ncbi fasta converter. Clearly downloaded txt file has more protein residues in one line as compared to normal fasta sequence has in one line.

Any suggestion how can i convert my sequence to the format in which blast deliver the results.

These first 2 sequences are from the .txt which we selected from blast result section.

>gi|733214911|ref|NP_001290023.1| betaine aldehyde dehydrogenase, chloroplastic [Beta vulgaris subsp. vulgaris]
MSMPIPSRQLFIDGEWREPIKKNRIPIINPSNEEIIGDIPAGSSEDIEVAVAAARRALKRNKGREWAATSGAHRARYLRA
IAAKVTERKDHFVKLETIDSGKPFDEAVLDIDDVATCFEYFAGQAEAMDAKQKAPVTLPMERFKSHVLRQPIGVVGLITP
WNYPLLMATWKIAPALAAGCTAVLKPSELASITCLEFGEVCNEVGLPPGVLNIVTGLGPDAGAPLAAHPDVDKVAFTGSS
ATGSKVMASAAQLVKPVTLELGGKSPIIVFEDVDIDQVVEWTMFGCFWTNGQICSATSRLLVHESIAAEFIDRLVKWTKN
IKISDPFEEGCRLGPVISKGQYDKIMKFISTAKSEGATILCGGSRPEHLKKGYFIEPTIISDISTSMQIWREEVFGPVLC
VKTFSSEDEALDLANDTEYGLASAVFSKDLERCERVSKLLESGAVWVNCSQPCFVHAPWGGIKRSGFGRELGEWGIENYL
NIKQVTSDISNEPWGWYKSP
>gi|806776646|ref|NP_001292971.1| betaine aldehyde dehydrogenase 1, chloroplastic [Jatropha curcas]
MAFPIPNRQLFIGGEWREPVLKKRIPIINPSTEESIGDIPAATAEDVEIAVEAAQKAFTRNKGRDWAFTSGAVRAKYLRA
IAAKITEKKAELAKLEAIDCGKPLDEAAWDIDDVAGCFEYYAGLAEGLDAKQKAPVSLPMETFKSYVLKEPIGVVALITP
WNYPLLMATWKVAPALAAGCTAILKPSELASVTCLELAEVCREVGLPPGVLNILTGLGPEAGAPLVSHPQVDKVAFTGST
ATGSRIMASAAQMVKPVSMELGGKSPIVVFEDVDLDKAAEWTAFGCFWTNGQICSATSRLLVHERIASEFLDRLVKWCKN
IKISDPLEEGCRLGPVVSGGQYDKVLKFISTAKSEGATILSGGARPKHLNKGFFIEPTIISDVNTSMQIWREEVFGPVLC
VKTFSSEDEAIELANDTHYGLGAAVISNDLERCDRVSKSFRAGIVWINCSQPCFCQAPWGGLKRSGFGRELGEWGLDNYL
SVKQVTQYISNEPWGWYQSPSKL

 

This is the sequences which I want to add in (searched by nucleotide search in ncbi website). But ncbi genome workbench keeps saying your sequence is not in fasta format.

>gi|381413280|gb|AFG28557.1| betaine aldehyde dehydrogenase [Atriplex canescens]
MAFPIPVRQLFIDGEWREPLLKNRIPIINPSTEEIIGDIPAATAEDVEVAVVAARKAFKRNKGRDWAATS
GAHRARYLRAIAAKITERKDHFVKLETLDSGKPLDEAVLDIDDVATCFEYFAGQAEALDAKQKAPVTLPM
DRFKSHVLRQPIGVVGLISPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLEFGEVCNEVGLPPGV
LNILTGLGPDAGAPIVSHPDIDKIAFFTGSSATGSKIMASAAQLVKRVTLELGGKSPVIMFEDIDIETAV
EWTLFGVFWTNGQICSATSRLLVHESIAAEFVDRMVKWTKNIKISDPFEEGCRLGPVISKGQYDKIMKFI
STAKSEGATILCGGSRPEHLKKGYYIEPTIITDITTSMQIWKEEVFGPVICVKTFSTEDEAIELANDTEY
GLAGAVFSKDLERCERVTKALEVGAVWVNCSQPCFVHAPWGGVKRSGFGRELGEWGIENYLNIKQVTSDI
SDEPWGWYKSP
blast ncbi • 1.3k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Shahzad10

Can you elaborate a bit more please?

  • What is this txt file download? Is it a file with BLAST output?
  • Can you give us the last 20 lines of this txt file?
  • What type of sequence are you trying to add to the file?
ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by RamRS24k
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