This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Find Mismatch And Gap Positions

Hi everyone,

I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the second step is troublesome for me.

Could you please suggest me the tools and methods that can be used to complete this task?

Thank you in advance!

blast fasta
• 8,940 views • link
updated by Ram Ram • written by biolab biolab

1 answer

I wrote something like this a few weeks ago: http://lindenb.github.io/jvarkit/BlastNToSnp.html

The program reads a BLASTN-XML file/stream , walk over the alignments and print the variations.

java -jar dist/blastn2snp.jar  blastn.xml | head
#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    .
• 150 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you, Pierre, the java program is cool.

• 0 views • link
written by biolab biolab

Hi Pierre, can you give me some details on how to compile this file?

I have downloaded and installed jvarkit following instructions here.

How can I compile and use this file:

my_local_dir/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java
• 0 views • link
updated by Ram Ram • written by Melia0787 • Melia0787

Dear Pierre

I need blastn2snp but i don't know how can i compile it. if possible explain more about that. Thanks

• 0 views • link
written by Mohammad Reza Bakhtiarizadeh Mohammad Reza Bakhtiarizadeh

Thank you Pierre!

Do you have a explanation/description of each column of the blastn2snp output? I want to understand something like:

REF(hit)    ALT(query)    blast.align_length    blast.hit.var    blast.query.var    blast.mid.var
CT      TG      35      AG       CA      ..  
GTC     T       37      GAC     A--     ...
"\t"        T       26      -           T       .
• 0 views • link
updated by Ram Ram • written by vitorlimac2 • vitorlimac2
  • REF: reference sequence
  • ALT: alternate sequence
  • blast.align_length: length of difference
  • blast.hit.var, blast.query.var, blast.mid.var: the blast lines (query/hit and difference line) seen in the blast output
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this