# Alignment with inserts and keeping the indexing of ref seq intact

Parts of sequences are given below-

Reference sequence (pre-alignment):

ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGT


Reference sequence (post-alignment) and below it is Sample sequence (post-alignment):

--------------------------------------------------------------------------------------------------attaaa---------ggtt------------------tataccttc---------ccaggtaacaaa-------------ccaacc-----aactttcgatctcttgtagatctgttctctaaacgaactttaaaatctgtgt
--------------------------------------------------------------------------------------------------------------------------------------------------------------taacaaa-------------ccaacc-----aactttcgatctcttgtagatctgttctctaaacgaactttaaaatctgtgt


I'm adding a simpler to interpret example-

Say the ref seq is aattaaatttgggggtttt and the sample seq is ttaaggggttaaatttgggggt--t. Then post-alignment, they will be like-

--aa----ttaaatttgggggtttt
ttaaggggttaaatttgggggt--t


Now, since my ref seq was

0    1    2    3    4    5    6    7    8    9    10   11   12   13   14   15   16   17   18
a    a    t    t    a    a    a    t    t    t    g    g    g    g    g    t    t    t    t


I want that post-alignment also, the indexing should be conserved-

           0    1                        2    3    4    5    6    7    8    9    10   11   12   13   14   15   16   17   18
-    -    a    a    -    -    -    -    t    t    a    a    a    t    t    t    g    g    g    g    g    t    t    t    t
t    t    a    a    g    g    g    g    t    t    a    a    a    t    t    t    g    g    g    g    g    t    -    -    t


I want to keep the indexing of the reference sequence conserved(i.e. the first base in ref seq post-alignment is a, second is t, third is t, etc.), like they do in standard softwares, and then I want to run some quick analysis on it, say to check for conservation of a (mono/di)-nucleotide at some positions. If anybody has some insight on how to do it the most efficient way(memory-wise and time-wise), then that'd be great. I use Python for my work.

• May be missing something, but is there a reason you can't map the reference index to an alignment index using e.g. a list with the reference positions in the alignment? e.g. ref_posns = [3, 4, 6] if only the 4th, 5th, 7th positions are ungapped in reference; you can use this to access only those aligned positions. There is probably a more standard way to do it than that, though I don't know it off top of head. It seems rather complex to introduce an indexing scheme that doesn't have an index for many positions of the alignment. May help to know what "standard softwares" you refer to. Sep 10 at 5:06