fasta-utils is a collection of command-line utilities for editing and viewing DNA and protein sequences. It is Free Software.

 $ cat myseq.fasta 

>  Example sequence
TTCATGTTGCATGGATTCTTTCAAGTTGCAGAGACTCCTC
GGAGGATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGT
TGCAGAGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCA
GTCTAGATAGTTTAG

 $ ./fastaorf < myseq.fasta 

>  Example sequence - ORF 1
ATGTTGCATGGATTCTTTCAAGTTGCAGAGACTCCTCGGA
GGATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGTTGC
AGAGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCAGTC

>  Example sequence - ORF 2
ATGGATTCTTTCAAGTTGCAGAGACTCCTCGGAGGATCCT
TCAAGTTGCAGAGACTCCTCGGATTCAAGTTGCAGAGACT
CCTCGGATCTTTCTTCACCGCCGTTCTTCAGTCTAGA

 $ ./fastaorf < myseq.fasta | ./fastatranslate 

>  Example sequence - ORF 1
MLHGFFQVAETPRRILQVAETPRIQVAETPRIFLHRRSSV

>  Example sequence - ORF 2
MDSFKLQRLLGGSFKLQRLLGFKLQRLLGSFFTAVLQSR

 $ ./fastadigest HindIII < myseq.fasta 

>  Example sequence fragment 1
TTCATGTTGCATGGATTCTTTCAAGTTGCAGAGACTCCTC
GGAGGATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGT
TGCAGAGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCA
GTCTAGATAGTTTAG

 $ ./fastadigest BamHI < myseq.fasta 

>  Example sequence fragment 1
TTCATGTTGCATGGATTCTTTCAAGTTGCAGAGACTCCTC
GGAG

>  Example sequence fragment 2
GATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGTTGCA
GAGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCAGTCT
AGATAGTTTAG

 $ cat primer-fwd.fasta primer-rev.fasta

> Forward primer 5'->3'
GCGGATTCGATTCTTTCAAGTTGCAGAGACTCCTC
> Reverse primer 5'->3'
GCGGATCCTGAAGAACGGCGGTGAAGAA

 $ ./amplify myseq.fasta primer-fwd.fasta primer-rev.fasta

>  Forward primer 5'->3'
GCGGATTCGATTCTTTCAAGTTGCAGAGACTCCTCGGAGG
ATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGTTGCAG
AGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCAGGATC
CGC


 $ (./amplify myseq.fasta primer-fwd.fasta primer-rev.fasta; cat 
myseq.fasta ) | kalign -e 100 2>/dev/null | ./fastastack 

  Forward primer 5'-3'..  -----GCGGATTCGATTCTTTCAAGTTGCAGAGACTCCTC  40
  Example sequence......  TTCATGTTGCATGGATTCTTTCAAGTTGCAGAGACTCCTC

  Forward primer 5'-3'..  GGAGGATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGT  80
  Example sequence......  GGAGGATCCTTCAAGTTGCAGAGACTCCTCGGATTCAAGT

  Forward primer 5'-3'..  TGCAGAGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCA  120
  Example sequence......  TGCAGAGACTCCTCGGATCTTTCTTCACCGCCGTTCTTCA

  Forward primer 5'-3'..  GGATCCGC-------  160
  Example sequence......  GTCTAGATAGTTTAG