Append two fasta sequences

Question

[tarakaramji]

I have two fasta files with different header and sequences and would like to append them one after the other in the same sequential order

Input: first file

>RNA1
AATGACGATGACGATGACAGAT
>RNA2
ATAGATGGGCAGTAGAGA

---

File2:

>mRNA1
ATGGAGATGAGAT
>mRNA2
AGATGGGGATGA

Ouput file should be

>RNA1:mRNA1
AATGACGATGACGATGACAGATATGGAGATGAGAT
>RNA2:mRNA2
ATAGATGGGCAGTAGAGAAGATGGGGATGA

[WouterDeCoster]

And what have you tried?

[tarakaramji]

I have tried the EMBOSS tool pasteseq which appends only the first sequence but does not retrieve the identifiers

Answer 1

[Pierre Lindenbaum]

assuming all fasta have two lines per record (name+seq)

paste f1.fasta f2.fasta | sed -e '/^>/s/\t>/:/' -e '/^[^>]/s/\t//'

[5heikki]

Alternatively: paste -d '' file1 file2 | sed 's/>/:/2' or e.g. paste -d '' file1 <(tr ">" ":" <file2)

[tarakaramji]

Thank you..Both works perfect!!