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Common File Formats
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Appendix 1B
DOI:
10.1002/0471250953.bia01bs16
Online Posting Date:
January, 2007 Abstract
This appendix discusses a few of the file formats frequently encountered in bioinformatics. Specifically, it reviews the rules for generating FASTA files and provides guidance for interpreting NCBI descriptor lines, commonly found in FASTA files. In addition, it reviews the construction of GenBank, Phylip, MSF and Nexus files.
Keywords: file format; FASTA; NCBI descriptor lines; GenBank; Phylip; MSF; Nexus
Figures
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Figure A.1B.1A sample FASTA file that contains the sequences for two homologous proteins, actophorin and yeast cofilin. Note that a greater-than sign (>) designates the beginning of each entry and that each of the lines of sequence contains less than 80 characters. -
Figure A.1B.2A sample GenBank record. Circled numbers identify the fields listed in Table -
Figure A.1B.3A sample PHYLIP-formatted file. The five sequences shown are HIV-1 and HIV-2 gag proteins from a variety of isolates. See text for details. -
Figure A.1B.4A sample MSF-formatted file. The five sequences shown are HIV-1 and HIV-2 gag proteins from a variety of isolates. See text for details. -
Figure A.1B.5A sample Nexus-formatted file. The five sequences shown are HIV-1 and HIV-2 gag proteins from a variety of isolates. See text for details.
Literature Cited
| Internet Resources | |
| http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi | |
| ReadSeq biosequence interconversion tool. | |
| http://www.ebi.ac.uk/clustalw | |
| ClustalW multiple sequence alignment interface. | |
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