Tag: EMBOSS

Petabase-scale sequence alignment catalyses viral discovery

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

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How to find the longest orf from a transcriptome

How to find the longest orf from a transcriptome 0 Hello, good day, sorry for the simplicity but, I have a super basic question. I have been trying to identify the longest ORF of a transcriptome for a long time, but from the previous failed attempts it seems that it…

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Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

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main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: sunp…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/p5-BioPerl-1.007007_1.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building biology/p5-BioPerl build started at Fri Oct 29…

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Remove Gaps from Multiple sequence alignment

Remove Gaps from Multiple sequence alignment 2 I want to remove col that contains gaps in the MSA file… Any sort of python code that helps me??? col Remove in MSA • 28 views Not sure if it’s python code but I know that trimAL can be used for this….

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the way to find pseudogenes in my scaffolds of genome

the way to find pseudogenes in my scaffolds of genome 3 Hello Recently, I assembled genome of a beetle living underground. My interest is searching pseudogenes (premature stop codon or frameshifts). I conducted tblastn using a few genes of model organisms (Tribolium) as query. But no premature stop codons were…

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Is it possible to use a loop to get the EMBOSS Merger function to work on multiple FASTA files?

Hello all, Previously, I posted about a question in a similar vein (see here) BUT now, 2 weeks later, I think I am nearly there! I plan to update that previous post and explain what I’ve done once I’ve tackled this final bit. (TL;DR my other question: I used the…

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Getting the same alignment from needle (emboss) and ggsearch36

Getting the same alignment from needle (emboss) and ggsearch36 0 I used to run ggsearch36 from the fasta package for NW alignment of proteins and now need to switch to needle from emboss, as ggsearch36 skips low-scoring alignments, whereas needle can return all. I’m looking for the correct configuration to…

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blast protein alignment

28 set blast protein alignment Posted at 20:44h in Sem categoria by BLAST applied the standard genetic code for Query, translating GTG into valine (V). The BLAST is a set of algorithms that attempt to find a short fragment of a query sequence that aligns perfectly with a fragment of…

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New biostar-tools metaport for FreeBSD

FYI, FreeBSD users can now install all the bioinformatics software referenced by the Biostar Handbook via FreeBSD ports. Everything except bedGraphToBigWig can be installed simply by running pkg install biostar-tools bedGraphToBigWig is part of ucsc-userapps, which cannot be redistributed for licensing reasons, so there is no binary package. However, the…

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Is it possible to isolate and merge overlapping hits from a BLAST search Aligned Fasta file?

Hello all, Hope you’re well. I started a PhD in Jan this year and frankly I am struggling. I’m coming into the second week of trying to figure out how to attempt this problem and it’s honestly starting to get to me a bit – the current task I’m working…

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Dnaman software manual

Dnaman software manual DNADynamo DNA Sequence Analysis SoftwareCLC Genomics Workbench – Qiagen They have sent a man to locate the key. He was making notes with a slim gold pen on a Gucci pad? When I married my husband, that all…

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EMBOSS transeq lines with “(REVERSE SENSE)” in not reverse sence translations(?)

EMBOSS transeq lines with “(REVERSE SENSE)” in not reverse sence translations(?) 0 Hi good day. Sorry, I have a silly doubt, if someone could help me I would really appreciate it. You see, I’m using EMBOSS’s transeq tool (something new for me) to translate an ORF file. When translating the…

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Failed to open filename / unable to read

Failed to open filename / unable to read – Ubuntu 1 Hii, i’ve been trying using primersearch from emboss on ubuntu but this keeps getting me the same error primersearch -seqall filename.fna -infile filename.txt -mismatchpercent 10 -outfile filename.primersearch Error: Failed to open filename ‘filename’ Error: Unable to read sequence ‘filename’…

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