Hello, I have a really annoying problem. I need to sort my BLAST results by percentage identity (%ident). Some of my sequences have an ambig. base in them. I want these sequences to show up as 100% identical to identical sequences that have a resolved ambig in them.
example: ATGC and ATGS = 100% ident ATGG and ATGS = 100% ident
because otherwise(?): ATGC and ATGS = 75% ident TTCG and ATGC = 75% ident
I know for sure that is correct, because my sequencing run has multiple gene copies that are amost (99,9%) identical, but sometimes I have two copies in one sequencing reaction and the basecaller calls an S, for example, if one paralogue has a C and the other one a G. This step is beyond my control. I have >100.000 sequences.
Thanks!
1 answer
Log in to answer this question.
-
Duplicates of the same gene in Orthogroup sequence files
written by niconps14 •
-
How to trim added sequences by library generation using SMART-ChIP-seq
written by almakarika5 •
-
Build consensus sequences from repeat masker output
written by Amaranta Remedios •
-
How produce a table with number of copies per unique sequence? (possible?)
written by angelaparody •
-
Parsing dataframe and sort a fasta file
written by Chvatil
-
Setting up blastn to retrieve FULL query sequence
written by tim.ivanov.92 •
-
cutadapt and paired-end reads when you don't know your adapter sequences...
written by beegrackle
-
Perl::ForkManager does not speed up ATCG calculation
written by BioGeek
-
Remove redundancy from GenBank plasmid database using cd-hit-est
written by wanderingstefan •
-
The reason two identical sequences have different accession numbers and different loci
written by Michel Edwar
I don't think that is possible unless you post-process your data. IUPAC codes are treated as mismatches in nucleotide alignment. See the help page here.