.. _ref_input_formats: =============== Input formats =============== The code has been tested for the following formats and versions for protein and nucleotide sequences: NCBI BLAST family ================= Sequence database search programs. See :ref:`ref_blast_rules` for details of `BLAST` processing by MView. BLAST+ ------ Modern BLAST can generate output in a number of formats; run `blastp -help` to see what is available. MView can process two of these: the default BLAST output format (also obtained with the BLAST command line option `-outfmt 0`) and a commented tabular format produced with `-outfmt 7`. MView support and testing is as follows. MView option: ``-in blast`` (with the default BLAST format) ========== ======= ======= ======= ====== ====== ====== ====== ====== ====== ====== ======= Program 2.2.25+ 2.2.28+ 2.2.31+ 2.3.0+ 2.4.0+ 2.5.0+ 2.6.0+ 2.7.1+ 2.8.1+ 2.9.0+ 2.10.0+ ========== ======= ======= ======= ====== ====== ====== ====== ====== ====== ====== ======= `blastp` ok ok ok ok ok ok ok ok ok ok ok `blastn` ok ok ok ok ok ok ok ok ok ok ok `blastx` . ok ok ok ok ok ok ok ok ok ok `tblastn` . ok ok ok ok ok ok ok ok ok ok `tblastx` . ok ok ok ok ok ok ok ok ok ok `psiblast` . ok ok ok ok ok ok ok ok ok ok `phiblast` . . . . . . . . . ok ok ========== ======= ======= ======= ====== ====== ====== ====== ====== ====== ====== ======= MView option: ``-in blast`` (with `-outfmt 7` tabular BLAST format) ========== ======= ======= ====== ====== ====== ====== ====== ====== ====== ======= Program 2.2.28+ 2.2.31+ 2.3.0+ 2.4.0+ 2.5.0+ 2.6.0+ 2.7.1+ 2.8.1+ 2.9.0+ 2.10.0+ ========== ======= ======= ====== ====== ====== ====== ====== ====== ====== ======= `blastp` ok ok ok ok ok ok ok ok ok ok `blastn` ok ok ok ok ok ok ok ok ok ok `blastx` ok ok ok ok ok ok ok ok ok ok `tblastn` ok ok ok ok ok ok ok ok ok ok `tblastx` ok ok ok ok ok ok ok ok ok ok `psiblast` ok ok ok ok ok ok ok ok ok ok `phiblast` . . . . . . . . ok ok ========== ======= ======= ====== ====== ====== ====== ====== ====== ====== ======= The main `-outfmt 7` fields or columns recognised by MView are: - `std` to report standard fields: `qaccver`, `saccver`, `pident`, `length`, `mismatch`, `gapopen`, `qstart`, `qend`, `sstart`, `send`, `evalue`, `bitscore`; - `qseq`, `sseq` to report the query and sbjct sequences; - `stitle` or `salltitles` to report the sbjct descriptions; - `qframe` to report the query frame; - `sframe` to report the sbjct frame. When running blast with tabular output, minimal field specifiers suitable for input to MView are: `blastp -outfmt '7 std qseq sseq stitle'` `blastn -outfmt '7 std qseq sseq stitle'` `blastx -outfmt '7 std qseq sseq stitle qframe'` `tblastn -outfmt '7 std qseq sseq stitle sframe'` `tblastx -outfmt '7 std qseq sseq stitle qframe sframe'` `psiblast -outfmt '7 std qseq sseq stitle'` Additional fields that are currently recognised by MView are: - `staxid` - `ssciname` - `scomname` - `sblastname` - `sskingdom` - `staxids` - `sscinames` - `scomnames` - `sblastnames` - `sskingdoms` If present, these are passed through in the format conversions (`-out fasta`, `-out pir`, `-out rdb`) and to the normal MView display mode where they appear as extra columns at the right margin of the alignment. Having very variable field widths they may appear badly aligned vertically. To disable them, use the `-label8` option. MView will silently ignore any fields other than those listed above. Note: There are some differences in the output (seen in BLAST `2.2.28+`) produced by the default BLAST format versus `-outfmt 7`. The latter lacks the list of ranked database hits and best scores and their associated fragment counts, N. Unfortunately this can obscure interpretation of the results when there are many alternative alignments for a given database hit (see :ref:`ref_blast_rules`) so that in certain cases the MView output will be slightly different; this is most noticeable with `tblastx`. Note: A strange behaviour has been seen with `psiblast 2.2.28+`, where the first database search produces many more hits than subsequent iterations including the final iteration when run using the default output format. Using `-outfmt 7` on the exact same search produces more consistent sets of hits. BLAST series 2.2 ---------------- MView option: ``-in blast`` ========== ===== ===== ===== Program 2.2.5 2.2.6 2.2.9 ========== ===== ===== ===== `blastp` ok ok ok `blastn` . ok ok `blastx` . ok ok `tblastn` . ok ok `tblastx` . ok ok `psiblast` . ok ok `phiblast` . ok ok ========== ===== ===== ===== BLAST series 2.0 ---------------- MView option: ``-in blast`` ========== ===== ===== ===== ===== ===== ====== ====== Program 2.0.2 2.0.4 2.0.5 2.0.6 2.0.9 2.0.10 2.0.14 ========== ===== ===== ===== ===== ===== ====== ====== `blastp` . ok ok . ok ok . `blastn` . ok ok . ok . ok `blastx` . . ok . ok . . `tblastn` . . ok . . ok . `tblastx` . . ok . . . . `psiblast` ok ok ok ok . ok . `phiblast` . . . . ok . . ========== ===== ===== ===== ===== ===== ====== ====== BLAST series 1.4 ---------------- MView option: ``-in blast`` ========== ===== ===== Program 1.4.7 1.4.9 ========== ===== ===== `blastp` ok ok `blastn` . ok `blastx` . ok `tblastn` . ok `tblastx` . ok ========== ===== ===== ------------------------------------------------------------------------------ WashU-BLAST family ================== Sequence database search programs. WU-BLAST series 2.0 ------------------- MView option: ``-in blast`` ========= ====== ====== === Program 2.0a13 2.0a19 2.0 ========= ====== ====== === `blastp` ok ok ok `blastn` . ok ok `blastx` . ok ok `tblastn` . ok ok `tblastx` . ok ok ========= ====== ====== === ------------------------------------------------------------------------------ Uni. Virginia FASTA family ========================== Sequence database search programs: FASTA series 36 --------------- MView option: ``-in uvfasta`` ========== ===== ====== ======= ====== ======= ======= ======= ======= ======= Program 36.07 36.3.3 35.3.5a 36.3.6 36.3.7b 36.3.8e 36.3.8f 36.3.8g 36.3.8h ========== ===== ====== ======= ====== ======= ======= ======= ======= ======= `fasta` ok ok . ok ok ok ok ok ok `fastx` . ok . ok ok ok ok ok ok `fasty` . . . ok ok ok ok ok ok `tfastx` . ok . ok ok ok ok ok ok `tfasty` . ok . ok ok ok ok ok ok `ssearch` . ok . ok ok ok ok ok ok `ggsearch` . ok . ok ok ok ok ok ok `glsearch` . ok . ok ok ok ok ok ok `fastm` . . expt expt expt expt expt expt expt `fasts` . . . expt expt expt expt expt expt `fastf` . . . expt expt expt expt expt expt `tfastm` . . . . expt expt expt expt expt `tfasts` . . . . expt expt expt expt expt `tfastf` . . . . expt expt expt expt expt ========== ===== ====== ======= ====== ======= ======= ======= ======= ======= where 'expt' indicates that MView parses and processes the format, but the results may not be particularly useful, hence 'experimental'. FASTA series 35 --------------- MView option: ``-in uvfasta`` ========== ===== Program 35.04 ========== ===== `fasta` ok `tfastx` ok `ssearch` ok `ggsearch` ok `glsearch` ok ========== ===== FASTA series 34 --------------- MView option: ``-in uvfasta`` ========== ======= Program 34.26.5 ========== ======= `fasta34` ok ========== ======= FASTA series 3.0 - 3.4 ---------------------- MView option: ``-in uvfasta`` ========== ====== ====== ====== ====== ====== ====== ====== ====== ====== ====== ====== Program 3.0t76 3.0t82 3.1t07 3.2t01 3.2t05 3.2t07 3.2t05 3.2t07 3.3t01 3.3t07 3.4t23 ========== ====== ====== ====== ====== ====== ====== ====== ====== ====== ====== ====== `fasta` ok . ok ok ok ok ok ok ok ok ok `fastx` . . . . . . . . . . ok `fasty` . . . . . . . . . . ok `tfasta` . . . . . . . . . . ok `tfastx` . ok . . . . . . . . ok `tfasty` . . . . . . . . . . ok `tfastxy` . . ok . . . . . . . . ========== ====== ====== ====== ====== ====== ====== ====== ====== ====== ====== ====== FASTA series 2 -------------- MView option: ``-in uvfasta`` ========== ==== ====== Program 2.0u 2.0u63 ========== ==== ====== `fasta` ok . `tfastx` . ok ========== ==== ====== FASTA series 1 -------------- MView option: ``-in uvfasta`` ========== ====== Program 1.6c24 ========== ====== `fasta` ok ========== ====== ------------------------------------------------------------------------------ CLUSTAL/aln =========== The CLUSTAL family of multiple sequence alignment programs produce 'aln' format. MView option: ``-in clustal`` ========= ==== ==== ==== === Version 1.60 1.70 1.83 2.1 ========= ==== ==== ==== === `CLUSTAL` ok ok ok ok ========= ==== ==== ==== === HSSP/Maxhom =========== The HSSP multiple sequence alignment format is produced by the MaxHom protein sequence and structure homology alignment program. MView option: ``-in hssp`` ======= ======== Version 1.0 1991 ======= ======== `HSSP` ok ======= ======== MAF === The UCSC Multple Alignment Format. MView option: ``-in maf`` MAF files contain distinct alignment blocks. By default, all blocks will be output. You can extract a particular block, say the second one, with ``-block 2``, or several with ``-block '1,2,7'``. FASTA ===== The classic FASTA (or Pearson) sequence file format. MView option: ``-in fasta`` MSF === The Wisconsin Package GCG Multiple Sequence File format. MView option: ``-in msf`` PIR === The Protein Information Resource sequence file format. MView option: ``-in pir`` plain ===== A simple multiple sequence alignment format. MView option: ``-in plain`` This is composed of rows of identifier and sequence in two columns like: .. raw:: html 
  identifier1   sequence1
  identifier2   sequence2
  identifier3   sequence3
and can contain comment lines starting with ``#``. Identifiers and sequences must not contain any whitespace as this is used to separate the columns. The sequences need not be aligned vertically, but they must all be the same length. Use ``-`` and/or ``.`` characters for gaps. Unsupported =========== A few other formats were implemented for specific use-cases and are not maintained: ============= =============== ============ Format MView option Status ============= =============== ============ MIPS-ALN ``-in mips`` experimental MULTAS/MULTAL ``-in multas`` experimental jnet -z ``-in jnet`` experimental ============= =============== ============ .. END