Finding differences between 2 fasta files

Question

[Jautis]

Hello, I have a two fasta files that represent large sections of a chromosome and I am wondering if there's a way to tell what bases differ between the two.

For example, a subsection could look like this:

Fasta 1:

>chr1 ATACGTGATCGAT.........AATCGT

Fasta 2:

>1 ATCCGTGATCGAT.........AATCGT

And I would want an output that says base 3 is different between the two.

Any ideas or advice would be great!

Answer 1

[Pierre Lindenbaum]

I wrote a blastn2snp: https://github.com/lindenb/jvarkit/wiki/BlastnToSnp

#query              hit                                                                                              hit-index  hsp-index  query-POS  hit-POS    STRAND  REF(hit)  ALT(query)  blast.align_length  blast.hit.var  blast.query.var  blast.mid.var
No definition line  Homo sapiens chromosome 6, alternate assembly CHM1_1.1                                           1          9          21         74567818   -       T         A           18                  A              T                .
No definition line  Homo sapiens chromosome 6, alternate assembly HuRef                                              2          9          21         71600901   -       T         A           18                  A              T                .
No definition line  Homo sapiens chromosome 6, GRCh37.p13 Primary Assembly                                           3          9          21         74401398   -       T         A           18                  A              T                .
No definition line  Homo sapiens chromosome 5, alternate assembly CHM1_1.1                                           4          1          7          107821121  -       A         G           28                  T              C                .
No definition line  Homo sapiens chromosome 5, alternate assembly CHM1_1.1                                           4          9          16         14262358   +       G         C           18                  G              C                .
No definition line  Homo sapiens chromosome 5, alternate assembly CHM1_1.1                                           4          13         8          132662461  -       T         C           18                  A              G                .
No definition line  Homo sapiens chromosome 5, alternate assembly CHM1_1.1                                           4          20         14         170329095  -       G         C           18                  C              G                .
No definition line  Homo sapiens chromosome 5, alternate assembly HuRef                                              5          1          7          103561224  -       A         G           28                  T              C                .
No definition line  Homo sapiens chromosome 5, alternate assembly HuRef                                              5          9          16         14234054   +       G         C           18                  G              C                .
No definition line  Homo sapiens chromosome 5, alternate assembly HuRef                                              5          13         8          128416747  -       T         C           18                  A              G                .
No definition line  Homo sapiens chromosome 5, alternate assembly HuRef                                              5          19         14         165993804  -       G         C           18                  C              G                .
No definition line  Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly                                           6          1          7          108388040  -       A         G           28                  T              C                .
No definition line  Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly                                           6          9          16         14262514   +       G         C           18                  G              C                .
No definition line  Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly                                           6          13         8          133231874  -       T         C           18                  A              G                .
No definition line  Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly                                           6          19         14         170896537  -       G         C           18                  C              G                .
No definition line  Homo sapiens chromosome 19, alternate assembly CHM1_1.1                                          8          13         18         54878835   -       A         C           18                  T              G                .
No definition line  Homo sapiens chromosome 19, alternate assembly CHM1_1.1                                          8          14         18         54999463   +       T         G           18                  T              G                .
No definition line  Homo sapiens chromosome 19, alternate assembly CHM1_1.1                                          8          15         21         55131801   -       G         A           18                  C              T                .
No definition line  Homo sapiens chromosome 19, alternate assembly HuRef                                             9          14         18         51207279   -       A         C           18                  T              G                .
No definition line  Homo sapiens chromosome 19, alternate assembly HuRef                                             9          15         18         51329261   +       T         G           18                  T              G                .
No definition line  Homo sapiens chromosome 19, alternate assembly HuRef                                             9          16         21         51461318   -       G         A           18                  C              T                .