[Back] [FAQ] Fasta header extractor and splitter - help page
 

The fasta header extractor and splitter are able to do two simple tasks:

1. Extract all the headers from a fasta file and output them in table format. This can be copied to excel for further editing. (The equivalent linux one-liner is: grep '>' sequencefile.fasta >outputfile.tsv
2. Split each header using a specified character. Typically, this is useful for sequences downloaded from genbank with headers like this:

   >gi|93102408|ref|NM_007988.3| Mus musculus fatty acid synthase (Fasn), mRNA
   >gi|75677473|ref|NM_001033326.1| Mus musculus dehydrogenase/reductase (SDR family) X chromosome (Dhrsx), mRNA
   >gi|41872630|ref|NM_004104.4| Homo sapiens fatty acid synthase (FASN), mRNA
   >gi|32455238|ref|NM_181755.1| Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript variant 2, mRNA
   >gi|32455237|ref|NM_005525.2| Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript variant 1, mRNA
   

   You may then use '|' as the splitting character, which will give you the following output:

   Original header	Splitted header fields
   gi|93102408|ref|NM_007988.3| Mus musculus fatty acid synthase (Fasn), mRNA	gi	93102408	ref	NM_007988.3	Mus musculus fatty acid synthase (Fasn), mRNA
   gi|75677473|ref|NM_001033326.1| Mus musculus dehydrogenase/reductase (SDR family) X chromosome (Dhrsx), mRNA	gi	75677473	ref	NM_001033326.1	Mus musculus dehydrogenase/reductase (SDR family) X chromosome (Dhrsx), mRNA
   gi|41872630|ref|NM_004104.4| Homo sapiens fatty acid synthase (FASN), mRNA	gi	41872630	ref	NM_004104.4	Homo sapiens fatty acid synthase (FASN), mRNA
   gi|32455238|ref|NM_181755.1| Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript variant 2, mRNA	gi	32455238	ref	NM_181755.1	Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript variant 2, mRNA
   gi|32455237|ref|NM_005525.2| Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript variant 1, mRNA	gi	32455237	ref	NM_005525.2	Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript variant 1, mRNA

   This output can be opened in excel and later reinserted into your sequences using the header replacer tool.