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<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><title>ChangeLog - FASTA v35</title><style type="text/css">body { margin-left: 6px; }.sidebar { font-size: 12px; font-family: sans-serif; text-decoration:none; background-color: #FFFFCC; }.fasta { font-family: sans-serif; }.fasta h2 { font-size: 16px; color: #000000 }.fasta h3 { font-size: 14px; color: #000000 }.fasta td {background-color: #FFFFCC }.fasta a { text-decoration: none; }.fasta li { margin-left:-1em }</style><head><body><div class=fasta><h2>ChangeLog - FASTA v35</h2><pre><small>$Name: fa35_03_06 $ - $Id: changes_v35.html,v 1.5 2008/02/19 08:50:13 wrp Exp $</small></pre><hr><h2>Summary - Major Changes in FASTA version 35 (August, 2007)</h2><ol><li>Accurate shuffle based statistics for searches of small libraries (or pairwise comparisons).<p/><li>Inclusion of <b>lalign35</b> (SIM) into FASTA3. Accurate statistics for<b>lalign35</b> alignments. <b>plalign</b> has been replaced by<b>lalign35</b> and <b>ps_lav</b>.</li><p/><li>Two new global alignment programs: <b>ggsearch35</b> and <b>glsearch35</b>.</li></ol><hr><h3>January 25, 2007</h3> Support protein queries and sequencelibraries that contain 'O' (pyrrolysine) and 'U' (selenocysteine).('J' was supported already). Currently, 'O' is mapped automatically to'K' and 'U' to 'C'.<p><h3>December 10, 2007</h3> Provide encoded annotation information with-m 9c alignment summaries. The encoded alignment information makes itmuch simpler to highlight changes in critical residues.<p><h3>August 22, 2007</h3> A new program is available, lav2svg, whichcreates SVG (Scalable Vector Graphics) output. SVG files are moreeasily edited with Adobe Illustrator than postscript (lav2ps) files.<p><h3>July 25, 2007 CVS fa35_02_02</h3>Change default gap penalties for OPTIMA5 matrix to -20/-2 from -24/-4.<p><h3>July 23, 2007</h3>Add code to support to support sub-sequence ranges for "library"sequences - necessary for fully functional prss (ssearch35) andlalign35. For all programs, it is now possible to specify a subset ofboth the query and the library, e.g.<pre>lalign35 -q mchu.aa:1-74 mchu.aa:75-148</pre>Note, however, that the subset range applied to the library will beapplied to every sequence in the library - not just the first - andthat the same subset range is applied to each sequence. This probablymakes sense only if the library contains a single sequence (this isalso true for the query sequence file).<p><h3>July 3, 2007 CVS fa35_02_01</h3>Merge of previous <tt><b>fasta34</tt></b> with development version <tt><b>fasta35</tt></b>.<h3>June 26, 2007</h3>Add amino-acid 'J' for 'I' or 'L'.<p>Add Mueller and Vingron (2000) J. Comp. Biol. 7:761-776 VT160 matrix,"-s VT160", and OPTIMA_5 (Kann et al. (2000) Proteins 41:498-503).<h3>June 7, 2007</h3><tt><b>ggssearch35(_t)</b></tt>, <tt><b>glsearch35(_t)</b></tt> can now use PSSMs.<h3>May 30, 2007 CVS fa35_01_04</h3><a name="ps_lav" />Addition of <tt><b>ps_lav</b></tt> -- which can be used to plot the lav output of<tt><b>lalign35 -m 11</b></tt>. <pre>lalign35 -m 11 | ps_lav</pre>replaces <tt><b>plalign</b></tt> (from <tt><b>FASTA2</b></tt>).<h3>May 2, 2007</h3>The labels on the alignment scores are much more informative (and morediverse). In the past, alignment scores looked like:<pre>>>gi|121716|sp|P10649|GSTM1_MOUSE Glutathione S-transfer (218 aa) s-w opt: 1497 Z-score: 1857.5 bits: 350.8 E(): 8.3e-97Smith-Waterman score: 1497; 100.0% identity (100.0% similar) in 218 aa overlap (1-218:1-218)^^^^^^^^^^^^^^</pre>where the highlighted text was either: "Smith-Waterman" or "bandedSmith-Waterman". In fact, scores were calculated in other ways,including global/local for <tt><b>fasts</b></tt> and <tt><b>fastf</b></tt>. With the addition of<tt><b>ggsearch35,</b></tt> <tt><b>glsearch35,</b></tt> and <tt><b>lalign35,</b></tt> there are many more ways tocalculate alignments: "Smith-Waterman" (ssearch and protein fasta),"banded Smith-Waterman" (DNA fasta), "Waterman-Eggert","trans. Smith-Waterman", "global/local", "trans. global/local","global/global (N-W)". The last option is a global global alignment,but with the affine gap penalties used in the Smith-Watermanalgorithm.<h3>April 19, 2007 CVS fa34t27br_lal_3</h3>Two new programs, <tt><b>ggsearch35(_t)</b></tt> and <tt><b>glsearch35(_t)</b></tt> are now available.<tt><b>ggsearch35(_t)</b></tt> calculates an alignment score that is global in thequery and global in the library; <tt><b>glsearch35(_t)</b></tt> calculates an alignmentthat is global in the query and local, while local in the librarysequence. The latter program is designed for global alignments to domains.Both programs assume that scores are normally distributed. Thisappears to be an excellent approximation for ggsearch35 scores, butthe distribution is somewhat skewed for global/local (glsearch)scores. <tt><b>ggsearch35(_t)</b></tt> only compares the query to library sequencesthat are beween 80% and 125% of the length of the query; glsearchlimits comparisons to library sequences that are longer than 80% ofthe query. Initial results suggest that there is relatively littlelength dependence of scores over this range (scores go downdramatically outside these ranges).<h3>March 29, 2007 CVS fa34t27br_lal_1</h3>At last, the <tt><b>lalign</b></tt> (SIM) algorithm has been moved from <b>FASTA21</b> to<b>FASTA35</b>. Currently, only <tt><b>lalign35</b></tt> is available(in May, a <tt><b><a href="#ps_lav">plalign</a></b></tt> equivalent was released).The statistical estimates for lalign35 should be much more accuratethan those from the earlier lalign, because lambda and K are estimatedfrom shuffles.In addition, all programs can now generate accurate statisticalestimates with shuffles if the library has fewer than 500 sequences.If the library contains more than 500 sequences, and the sequences arerelated, then the -z 11 option should be used.<hr><a href="changes_v34.html">FASTA v34 Change Log</a><p> </p></div></body></html>⌨️ 快捷键说明
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