The FASTA package - protein and DNA sequence similarity searching and alignment programs
Changes in fasta-36.3.8i Sept, 2021
- Enable translation table -t 9 for Echinoderms. This bug has existed since alternate translation tables were first made available.
Changes in fasta-36.3.8i May, 2021
- Add an option, -Xg, that preserves the gi|12345 string the score summary and alignment output.
Changes in fasta-36.3.8i Nov, 2020
fasta-36.3.8i (November, 2020) incorporates the SIMDe (SIMD-everywhere, https://github.com/simd-everywhere/simde/blob/master/simde/x86/sse2.h) macro definitions that allow the smith_waterman_sse2.c, global_sse2.c, and glocal_sse2.c code to be compiled on non-Intel architectures (currently tested on ARM/NEON). Many thanks to Michael R. Crusoe (https://orcid.org/0000-0002-2961-9670) for the SIMDE code converstion, and to Evan Nemerson for creating SIMDe.
The code to read FASTA format sequence files now ignores lines with '#' at the beginning, for compatibility with PSI Extended FASTA Format (PEFF) files (http://www.psidev.info/peff).
Changes in fasta-36.3.8h May, 2020
fasta-36.3.8h (May 2020) fixes a bug that appeared when multiple query sequences were searched against a large library that would not fit in memory. In that case, the number of library sequences and residues increased by the library size with each new search.
More consistent formats for *** ERROR and *** Warning messages.
Corrections to code to address compiler warnings with gcc8/9.
addition of 's' option to show similarity in -m8CBls (or -m8CBs, -m8CBsl) and 'd' option to show raw (unaligned) domain information.
Changes in fasta-36.3.8h February, 2020
- The license for Michael Farrar's Smith-Waterman sse2 code and global/glocal sse2 code is now open source (BSD), see COPYRIGHT.sse2 for details.
Changes in fasta-36.3.8h August, 2019
- Modifications to support makeblastdb format v5 databases. Currently, only simple database reads have been tested.
Changes in fasta-36.3.8h March, 2019
Translation table 1 (
-t 1) now translates 'TGA'->'U' (selenocysteine).
New script for extracting DNA sequences from genomes (
scripts/get_genome_seq.py). Currently works with human (hg38), mouse (mm10), and rat (rn6).
Changes in fasta-36.3.8h January, 2019
tfastxsearches done with the
-t toption (which adds a
*to protein sequences so that termination codons can be matched), did not work properly with the
VTseries of matrices, particularly
VT10. This has been fixed.
New features: Both query and library/subject sequences can be generated by specifying a program script, either by putting a
!at the start of the query/subject file name, or by specifying library type
fasta36 \\!../scripts/get_protein.py+P09488+P30711 /seqlib/swissprot.faor
fasta36 "../scripts/get_protein.py+P09488+P30711 9" /seqlib/swissprot.fawill compare two query sequences,
P30711, to SwissProt, by downloading them from Uniprot using the
get_protein.pyscript (which can download sequences using either Uniprot or RefSeq protein accessions). Often, the leading
!must be escaped from shell interpretation with
New scripts that return FASTA sequences using accessions or genome coordinates are available in
get_refseq.py can download either protein or mRNA RefSeq entries.
get_up_prot_iso_sql.py retrieves a protein and its isoforms from a MySQL database.
get_genome_seq.py extracts genome sequences using coordinates from local reference genomes (
mm10 included by default).
Changes in fasta-36.3.8h December, 2018
ann_exons_up_sql.pl now include the option
--gen_coord which provides the associated genome coordinate (including chromosome) as a feature, indicated by
'<' (start of exon) and
'>' (end of exon).
Changes in fasta-36.3.8h released November, 2018
fasta-36.3.8h provides new scripts and modifications to the
fasta programs that normalize the process of merging sub-alignment scores and region information into both FASTA and BLAST results. To move BLASTP towards FASTA with respect to alignment annotation and sub-alignment scoring:
blastp_annot_cmd.shruns a blast search, finds and scores domain information for the alignments, and merges this information back into the blast output
.htmlfile. This script uses:
annot_blast_btab2.pl --query query.file --ann_script annot_script.pl --q_ann_script annot_script.pl blast.btab_file > blast.btab_file_ann(a blast tabular file with one or two new fields, an annotation field and (optionally with --dom_info) a raw domain content field.
merge_blast_btab.pl --btab blast.btab_file_ann blast.html > blast_ann.html(merge the annotations and domain content information in the
blast.btab_file_annfile together with the standard blast output file to produce annotated alignments.
- In addition,
rename_exons.pyis available to rename exons (later other domains) in the subject sequences to match the exon labeling in the aligned query sequence.
relabel_domains.pycan be used to adjust color sets for homologous domains.
There is also an equivalent
fasta_annot_cmd.shscript that provides similar funtionality for the FASTA programs. This script does not need to use
annot_blast_btab2.plto produce domain subalignment scores (that functionality is provided in FASTA), but it also can use
rename_exons.pyto modify the names of the aligned exons/domains in the subject sequences.
To support the independence of the
fastaoutput from html annotation, the FASTA package includes some new options:
-m 8CBLoption includes query sequence length and subject sequence length in the blast tabular output. In addition, if domain annotations are available, the raw domain coordinates are provided in an additional field after the annotation/subalignment scoring field.
-m 8CBlprovides the sequence lengths, but does not add the raw domain coordinates.
-Xaoption prevents annotation information from being included in the html output -- it is only available in the
-m 8CBL/l) output
To reduce problems with spaces in script arguements, annotation scripts with spaces separating arguments can use '+' instead of ' '.
fasta_annot_cmd.shscript produces both a conventional alignment on
-m 8CBLalignment, which is sent to a separate file, which is separated from the
-m F8CBLoption with a
Changes in fasta-36.3.8g released 23-Oct-2018
(Oct. 2018) Improvements to scripts in the
--clustaloption produces a "CLUSTALW (1.8)", which is required for some downstream programs
--trunc_accoption removes the database and accession from identifiers of the form:
--min_alignoption specifies the fraction of the query sequence that must be aligned
(q_end-q_start+1)/q_length)Together, these changes make it possible for the output of
m89_btop_msa2.plto be used by the EMBOSS program
A more general implementation of
psisearch2_msa_iter.sh, which does
psisearch2one iteration at a time, and a new equivalent
psisearch2_msa_iter_bl.sh, which uses
psiblastto do the search.
- (Oct. 2018) A small restructuring of the
make/Makefilesto remove the
-lzdependence for non-debugging scripts (and add it back when -DDEBUG is used).
Changes in fasta-36.3.8g released 5-Aug-2018
(Apr 2018) incorporation of
-t t1termination codes ("*") in
-m 8CC, and
-m9Cso that aligned termination codons are indicated as
(Mar 2018) Updates to scripts/annot_blast_btop2.pl to provide subalignment scoring for blastp searches (BLOSUM62 only). (see doc/readme.v36)
(Feb. 2018) a new extended option,
-XB, which causes percent identity, percent similarity, and alignment length to be calculated using the BLAST model, which does not count gaps in the alignment length.
see readme.v36 for other bug fixes.
Changes in fasta-36.3.8g released 31-Dec-2017
(December, 2017) -- Make statistical thresholds more robust for small E()-values with normally distributed scores (
(September, 2017) Treat lower-case queries with no upper-case residues as uppercase with
(May, 2017) Improvements/fixes to sub-alignment scoring strategies.
Improvements/fixes to psisearch2 scripts.
For more detailed information, see