Valid fasta format - Revision history

RobEdwards at 21:59, 14 May 2008

2008-05-14T21:59:21Z

RobEdwards at 21:59, 14 May 2008

2008-05-14T21:59:04Z

RobEdwards at 21:58, 14 May 2008

2008-05-14T21:58:35Z

RobEdwards at 21:58, 14 May 2008

2008-05-14T21:58:01Z

RobEdwards at 18:54, 4 October 2007

2007-10-04T18:54:28Z

RobEdwards at 18:53, 4 October 2007

2007-10-04T18:53:58Z

New page

One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things:

# There should be no spaces or tabs at the start or ends of the lines
# The identifier line should begin with a greater than sign ">", and only one line is allowed
# Typically most bioinformatics applications use the first word after the > as the identifier for the sequence. Its nice (but not essential) if this is unique
# In the sequence lines (not header lines), spaces and numbers are removed.

Examples of valid fasta

>sequenceid
gatgcagcatgcagctagcagcgacggactac...
>1 this is a sequence that i know something about
gatgcagcatgcagctagcagcgacggactac...

Examples of invalid fasta

>sequenceid
This is a comment about the sequence
gatgcagcatgcagctagcagcgacggactac...
''Pleae don't include comments in the sequence data''

>sequenceid
gatgcagcatgcagctagcagcgacggactac...
''please don't have spaces before the > in the identifier''

fasta is probably the most common sequence format because it is relatively compact, and very easy to parse.

There is more information about the fasta format at:
# [http://en.wikipedia.org/wiki/Fasta_format Wikipedia]
# [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI]

@@ Line 28: / Line 28: @@
     >sequenceid\rgatgcagcatgcagctagcagcgacggactac...
-   ''this is a sequence that has been edited in a mac.''
+    ''This is a sequence that has been edited in a mac.''
      ''We try to fix them, because we're mac users too, but can't always.''
      ''Please make sure you save using UNIX format if you are using a mac".

@@ Line 28: / Line 28: @@
     >sequenceid\rgatgcagcatgcagctagcagcgacggactac...
-    ''this is a sequence that has been edited in a mac.
+    ''this is a sequence that has been edited in a mac.''
-     We try to fix them, because we're mac users too, but can't always.
+     ''We try to fix them, because we're mac users too, but can't always.''
-     Please make sure you save using UNIX format if you are using a mac".
+     ''Please make sure you save using UNIX format if you are using a mac".

← Older revision		Revision as of 21:58, 14 May 2008
Line 28:		Line 28:

	>sequenceid\rgatgcagcatgcagctagcagcgacggactac...		>sequenceid\rgatgcagcatgcagctagcagcgacggactac...
−	''this is a sequence that has been edited in a mac. We try to fix them, because we're mac users too, but can't always. Please make sure you save using ~~newlines (sometimes called~~ UNIX format) if you are using a mac".	+	''this is a sequence that has been edited in a mac.
		+	We try to fix them, because we're mac users too, but can't always.
		+	Please make sure you save using UNIX format if you are using a mac".

← Older revision		Revision as of 21:58, 14 May 2008
Line 26:		Line 26:
	gatgcagcatgcagctagcagcgacggactac...		gatgcagcatgcagctagcagcgacggactac...
	''please don't have spaces before the > in the identifier''		''please don't have spaces before the > in the identifier''
		+
		+	>sequenceid\rgatgcagcatgcagctagcagcgacggactac...
		+	''this is a sequence that has been edited in a mac. We try to fix them, because we're mac users too, but can't always. Please make sure you save using newlines (sometimes called UNIX format) if you are using a mac".

← Older revision		Revision as of 18:54, 4 October 2007
Line 1:		Line 1:
−	One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded. In particular, please check the following things:	+	One of the most frequent errors with uploading the data is incorrect file format. We recommend fasta format for all the sequence data to be uploaded.
		+
		+	In particular, please check the following things:

	# There should be no spaces or tabs at the start or ends of the lines		# There should be no spaces or tabs at the start or ends of the lines