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Version 2.0 original
Version 2.1 released 03-24-04 by P.Ng
Added info_on_seqs "-" option to print out SIFT scores for entire protein.
Updated Alignment.c to prevent segmentation fault if multiple blank lines in
PSI-BLAST output file.
Version 2.1.1 released 01-10-07
No software changes. Changed README notes for accurate description on how
to run info_on_seqs by commandline.
Version 2.1.2 released 05-31-07
Change cccb to compile correctly with blimps 8
Change directons for sed and to download blimps 8
Version 3.0 released 3-19-08
Allow sequence retrieval from BLink
(This uses precomputed NCBI BLAST searches, and can be a huge timesaver)
Version 4.0 released 11-23-09
Allows exome scale single nucleotide variant characterization and prediction (SIFT_exome_nssnvs.pl)
Allows exome scale insertion/deletion variant characterization (SIFT_exome_indels.pl)
For instructions on how to use these tools, please see README_4.0
VERSION 4.0.1 released 01-22-10
Retrieving sequences by gi reported to not be working. Fix get_BLINK_seq.pl script .
Added SIFT_intersect_cds.pl so that users can filter out noncoding variants out of
large genomic variant genomic lists.
VERSION 4.0.2 released February 5, 2010
Fix strand orientation in snv_db_engine.pl
VERSION 4.0.3 released March 8, 2010
Change snv_db_engine to match SIFT website
Clarify instructions for SIFT_exome_indels.pl and SIFT_intersect_cds.pl
Make available web tools
VERSION 5.1.1, released January 17, 2014
SIFT Standalone v5.1.1 release - Minor bug fixed for SIFT indels tool
VERSION 5.2.0, released July 12, 2014
SIFT 5.2.0 released. Code has been updated to be compatible with later versions of BLAST (tested on 2.2.28+)
VERSION 5.2.1, released August 11, 2014
SIFT 5.2.1 released. Fixed bug to increase coverage. BLAST results on sequences with repetitive sequences were not always parsed correctly and would give a segmentation fault. Bug fix will increase number of sequences with predictions. Prediction scoring remains unchanged.
VERSION 6.0.0, released August 1, 2016
Released SIFT 6.0.0. This release only features "Single Protein Tools", and includes BLIMPS code for easier installation.
VERSION 6.0.1, released August 15, 2016
Released SIFT 6.0.1. Fixes a bug for parsing BLAST output. This release only features "Single Protein Tools", and includes BLIMPS code for easier installation.
VERSION 6.1.0, released December 5, 2016
Changed blimps code sequences.h sequence_struct->undefined from int to double so that percent identity is compared correctly
VERSION 6.2.0, released December 12, 2016
Changes to get_BLink_seq.pl : (1) https protocol for querying NCBI instead of htt (2) added "complete genomes" option (cg_only) (3) limit to 399 sequences, so that with query, it's 400 sequences.
VERSION 6.2.1, Fixed bus error by initializing variable. Also changed code to allow compilation without warnings.
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