<div dir="rtl"><div dir="ltr"><font face="arial, helvetica, sans-serif">Hi all,</font></div><div dir="ltr"><font face="arial, helvetica, sans-serif"><br></font></div><div dir="ltr"><font face="arial, helvetica, sans-serif">I have a pairwise alignment of protein sequences, created with <span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(102,0,102)">Bio</span><span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(102,102,0)">.</span><span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)">pairwise2, something like this:</span></font></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><br></span></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><pre class="" style="padding:10px;font-family:Monaco,Menlo,Consolas,'Courier New',monospace;color:rgb(51,51,51);border-radius:5px;margin:8px;line-height:10.8333330154419px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;border:1px solid rgb(198,201,204);background-image:-webkit-linear-gradient(top,rgb(248,248,249) 0%,rgb(236,240,243) 100%);background-repeat:initial"><span class="" style="color:rgb(0,0,0)">C</span><span class="" style="color:rgb(102,102,0)">-</span><span class="" style="color:rgb(0,0,0)">GGLK</span><span class="" style="color:rgb(102,102,0)">-</span><span class="" style="color:rgb(0,0,0)">GAPFLAC
</span><span class="" style="color:rgb(102,102,0)">||||||||||||||</span><span class="" style="color:rgb(0,0,0)">
CHG</span><span class="" style="color:rgb(102,102,0)">--</span><span class="" style="color:rgb(0,0,0)">KTGASFLQC</span></pre></span></div><div dir="ltr"><font face="arial, helvetica, sans-serif">I would like to <span style="color:rgb(51,51,51);font-size:13px;line-height:10.8333330154419px">know which position in the subject sequence is aligned to which position in the query sequence. </span><span style="color:rgb(51,51,51);font-size:13px;line-height:10.8333330154419px">In this example if the top sequence is the subject than I would like to know that position 1 in subject is aligned to position 1 in query, 2 is aligned to 3, 5 to 4, 6 to 6 etc...</span></font></div><div dir="ltr"><span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif"><br></font></span></div><div dir="ltr"><span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif">Does Biopython have this functionality, or do I have to write my own function? Any suggestions?</font></span></div><div dir="ltr"><span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif"><br></font></span></div><div dir="ltr"><span class="" style="font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif">Thanks!</font></span></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><br></span></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><br></span></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><br></span></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><br></span></div><div dir="ltr"><span class="" style="font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;line-height:10.8333330154419px;white-space:pre-wrap;color:rgb(0,0,0)"><br></span></div></div>