How To Use The Recon Package To Identify Repeat Families From Genomic Sequences
I'm trying to learn RECON and am experimenting using chr22. My steps so far, roughly:Make blast database from chr22.faBLAST chr22.fa against its own databaseRun MSPCollect.pl (RECON provided script) to...
View ArticleBlast Execution Problem
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
View ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
View ArticleLocal Blast: Querying A Single Sequence Without Input File. Possible ?
Hi,When using BLASTALL by command line, is there any way of querying BLASTALL without using any input file but a directly a sequence ?I would like to do something like:blastall -n blastn -d MyBud.fna...
View ArticleHow Does The Blast Algorithm Work ?
hello could someone please point me to some article that explains how the blast algorithm works.
View Article[Fastacmd] How To Retrieve Sequence From Blast Db
Let's say I have multifasta with protein sequences having internal IDs (integer)>1234 MGKL...*I build blast db using:formatdb -i infile.fa -pF -n someDBBut then, I'm unable to retrieve sequence from...
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
View ArticleRemove species from nr
Hi, I'm using a local installation of blast with the nr database. I'm mostly looking for viral species, but the viral refseq database misses some hits compared to a full nr search, but the nr search...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleBamfile Coordinates
I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a...
View ArticleAnnotating Rna-Seq Data Using A Reference Genome.
I have RNA-seq reads from a non-model organism. I used cufflinks to identify transcripts. Is there an existing pipeline to BLAST these transcripts to a model organism's proteins to identify orthologs?
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
View ArticleComparing Protein Datasets By Sequence
Hi, I have several proteins datasets which I want to compare. I want to use sequence identity (not IDs) in order to count the number of shared proteins between each dataset pair.I want to identify...
View ArticleOpening A Fasta File In Windows
Hi all,I am a beginner with Blast+.I am using Windows.My aim as of now is to download the nr protein sequence in Fasta format and then format it using makeblastdb.then extract the first 1000 characters...
View ArticleBlastp Against Human Proteome
Hey guys,I have a list of gi's for about 10000 protein sequences all from vertebrate species. I want to blast these sequences against non-redundant protein sequences only from humans. I will run the...
View ArticlePython/Perl Script For Defining Minimum Coverage Of Blast Match
Hi - does anyone know of a script that allows for a blast result to be filtered by the minimum total coverage of the query/subject that the alignment/s represent?I'm imagining a script that calculates...
View ArticleLooking For Frequency Of A Very Specific Rna Editing Event In Publicly...
I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a...
View ArticleScript To Submit And Manage Blast Jobs On A Cluster?
Hi,I make use of a local cluster (managed through LSF) to BLAST large sequence sets. I wrote a basic script to split a fasta file and submit each part as a different BLAST job. Does anyone know of such...
View ArticleBl2Seq/Blastall And The E Value Help
I am using bl2seq(2.2.25) to blastn two fasta files. I am not sure I fully understand how the (-e) parameter works. I thought the -e parameter was a cut off e-value and would therefore show all results...
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