Hi you would need to use a different sequence assembly software for this. Mauve does not provide a consensus output sequence that you can extract and download. It just aligns and visualises the genomes.
Hello, apologies for the later reply, I have been away. After rearranging, any colored blocks in the first, reference genome should be connected by lines to similarly colored blocks in the other genomes. The lines and colours show which regions are the same or similar between the genomes. Its hard to say without seeing your alignment, but, if the blocks are all one colour, it might indicate the compared genomes are organised very similarly?
im running Mauve in command line (linux) and having trouble to align around 50 whole genome sequences. i did paralell computing using 8 cores and tried speed up a process, but everytime i end up with error. any ideas? thanks
Hi Leon, it would be best to find someone running MAUVE on Linux and ask them. I did see a discussion of the MAUVE/Linux/error topic on the Biostars website if this helps. www.biostars.org/p/159917/ Good luck and I hope you get it sorted out.
thanks for the video, what if you were working with an species that has never been sequence before... what would you use as a reference sequence? a similar species?
Hi, my thoughts on this are - yes, also you would probably want to make sure the sequenced genome of your species of interest was assembled into a single chromosomal sequence first. Paraphrased from the Mauve website: “Mauve works best on closely related organisms. As genomes diverge from ancestral species their chromosomes undergo numerous rearrangements. Even after long evolutionary periods, many sequences remain but these can be present in different arrangements from one species to the next. In Mauve, the Localized Co-Linear Blocks (LCBs - colored blocks) are regions of the chromosome that appear to be conserved across the species being analyzed”. Using Mauve you could align a number of whole / similar genomes against the genome you are interested in.
@@eswinipi Hi, when in Mauve, press the “file” tab and select “align with progressive Mauve” below the “sequences to align” box there is a box marked “output”. If you press on the tab with the three dots next to the output box, a new window will appear asking you where you want to save your Mauve output files to. Once you have decided where to save the output files, they will save to that location automatically once the alignment has completed. You can save your output files to wherever you want really, but I find it easier using a new folder specifically for my alignments e.g. I create a new folder and call it something like alignments on the deskstop. When you want to open a past alignment, open Mauve and press the “file” tab and then “open alignment”.
@@genomeprojects Thank you so so much! can your reference genome be in .fasta file instead? whenever I try a .gb file it keeps giving me and "exit error 3" and yes I already saw my new aligments saved on my new created folder, I was just wondering if Mauve saves those new aligments in .fasta or .gb files.
@@eswinipi Hi, if you align Fasta files, you might not have any annotations in your alignment - all that you will be able to see is the aligned nucleotide sequences (no gene names etc..). If you use a GenBank file make sure it is the full GenBank file. E.g. If exporting a genome from NCBI select “GenBank full” rather than export “GenBank” or you will not have any sequence / annotation information in the file. If you have the correct “full” GenBank files, (not sure if) exit error 3 might be to do with running out of memory to complete the alignment task, you could try aligning only a couple of genomes first just to check. I have had a look at the output files from a completed alignment, although one of the larger size files can be opened in notepad and contains genome sequences in a Fasta format, I don’t think the output files themselves are much use outside of Mauve - I have not used these for anything else myself that is. Hope this helps.
Hi Genome Projects, Thanks so much for this tutorial. I have been using the Mauve genome analysis software lately but got stuck with which file type to open some result output formats after alignment. Particularly these files: SNPs, Permutation, Orthologs and Gaps. I have exported them to my PC, but do not know which file to open them with. Any assistance from you?
Hi, these are tab-delimited files. If you open Excel, then go to: File - open, and select either your SNP, Permutation, Ortholog or Gap file. This should open them in Excel, although you may need to format the data into columns when opening Excel for some of these. Alternatively you can open these files in Notepad then copy and paste the data into a blank Excel sheet, I find this a good option.
Dear Genome Projects, thank you very much for your video. I have tried to use mauve but I got an error (Exited with error code: -1073741819 ). Could I please get some help? Greetings from Argentina Ceci
Hi, not exactly sure about the error code. Info on the web indicates this might be associated with Windows components needing an update. I would first try putting any files to align on your desktop and working from there - if they are not already. Also try only aligning a couple of genomes first (if you have a lot) in case the error relates to your memory availability for MAUVE to complete the tasks. You could also try "right click on MAUVE" and troubleshoot compatibility. Hope this helps,
Hi! I wanna ask, I already aligned 2 genome sequences and wanted to find a specific gene/product in the sequence navigator but still no results came out. Any suggestions or solutions? Thank you.
Might depend what is is annotated as in your reference genome. If you can find the gene in your GenBank file this will also give you a Locus Tag that you can search for in MAUVE rather than search for gene or product. You can also find the coordinates of the gene from your annotation file and then zoom into that region in MAUVE.
@@cindyoctaviana9842 Your reference genome would normally be a complete genome I.e. a single annotated chromosome assembly - not a genome in numerous contigs. When using progressive Mauve to align a genome to a reference, it is best to add the reference first - there is however an option to move the order of the genomes after the alignment has completed. On the far left of the alignments there should be something that looks like: ^ - R V You can use this to move the positions of the genomes and set which you want to use as a reference after alignment has completed.
Error in Mauve? I would check the file types you are using Genbank or FASTA etc.. as well as where you are saving the output files - in case there is a problem saving them to the location you have stated. Just a thought, I had issues once saving them to a USB.
@@louismostert2650 if you are downloading the genome from NCBI - when on the page with the genome. In the "send to" drop down menu @ top of page, try selecting: complete record then select the destination as "file". Then in the drop down "format" options select GenBank (full) rather than just GenBank. Saving the file in this format has worked for me in the past.
Hi you would need to use a different sequence assembly software for this. Mauve does not provide a consensus output sequence that you can extract and download. It just aligns and visualises the genomes.
Thank you for the useful video.
Why does the resulting alignment appear red when I reorder the alignment genome?
Hello, apologies for the later reply, I have been away. After rearranging, any colored blocks in the first, reference genome should be connected by lines to similarly colored blocks in the other genomes. The lines and colours show which regions are the same or similar between the genomes. Its hard to say without seeing your alignment, but, if the blocks are all one colour, it might indicate the compared genomes are organised very similarly?
im running Mauve in command line (linux) and having trouble to align around 50 whole genome sequences. i did paralell computing using 8 cores and tried speed up a process, but everytime i end up with error. any ideas? thanks
Hi Leon, it would be best to find someone running MAUVE on Linux and ask them. I did see a discussion of the MAUVE/Linux/error topic on the Biostars website if this helps. www.biostars.org/p/159917/
Good luck and I hope you get it sorted out.
thanks for the video, what if you were working with an species that has never been sequence before... what would you use as a reference sequence? a similar species?
Hi, my thoughts on this are - yes, also you would probably want to make sure the sequenced genome of your species of interest was assembled into a single chromosomal sequence first.
Paraphrased from the Mauve website: “Mauve works best on closely related organisms. As genomes diverge from ancestral species their chromosomes undergo numerous rearrangements. Even after long evolutionary periods, many sequences remain but these can be present in different arrangements from one species to the next. In Mauve, the Localized Co-Linear Blocks (LCBs - colored blocks) are regions of the chromosome that appear to be conserved across the species being analyzed”. Using Mauve you could align a number of whole / similar genomes against the genome you are interested in.
@@genomeprojects thank you so much, and how would you save the new align sequence?
@@eswinipi Hi, when in Mauve, press the “file” tab and select “align with progressive Mauve” below the “sequences to align” box there is a box marked “output”. If you press on the tab with the three dots next to the output box, a new window will appear asking you where you want to save your Mauve output files to.
Once you have decided where to save the output files, they will save to that location automatically once the alignment has completed.
You can save your output files to wherever you want really, but I find it easier using a new folder specifically for my alignments e.g. I create a new folder and call it something like alignments on the deskstop.
When you want to open a past alignment, open Mauve and press the “file” tab and then “open alignment”.
@@genomeprojects Thank you so so much! can your reference genome be in .fasta file instead? whenever I try a .gb file it keeps giving me and "exit error 3" and yes I already saw my new aligments saved on my new created folder, I was just wondering if Mauve saves those new aligments in .fasta or .gb files.
@@eswinipi Hi, if you align Fasta files, you might not have any annotations in your alignment - all that you will be able to see is the aligned nucleotide sequences (no gene names etc..). If you use a GenBank file make sure it is the full GenBank file.
E.g. If exporting a genome from NCBI select “GenBank full” rather than export “GenBank” or you will not have any sequence / annotation information in the file.
If you have the correct “full” GenBank files, (not sure if) exit error 3 might be to do with running out of memory to complete the alignment task, you could try aligning only a couple of genomes first just to check.
I have had a look at the output files from a completed alignment, although one of the larger size files can be opened in notepad and contains genome sequences in a Fasta format, I don’t think the output files themselves are much use outside of Mauve - I have not used these for anything else myself that is. Hope this helps.
Hi Genome Projects,
Thanks so much for this tutorial.
I have been using the Mauve genome analysis software lately but got stuck with which file type to open some result output formats after alignment. Particularly these files: SNPs, Permutation, Orthologs and Gaps. I have exported them to my PC, but do not know which file to open them with.
Any assistance from you?
Hi, these are tab-delimited files. If you open Excel, then go to: File - open, and select either your SNP, Permutation, Ortholog or Gap file. This should open them in Excel, although you may need to format the data into columns when opening Excel for some of these.
Alternatively you can open these files in Notepad then copy and paste the data into a blank Excel sheet, I find this a good option.
Okay. I will try this, and let you know my experience. Thank you!
It worked! Thanks very much.
@@greaterk.oyejobi7893 Hi; to find orthologs, is this working well?
Hii, my polished genome and the reference genome was apmost the same. Did i do anything wrong? Pls help
Hi, just wondering what species are you working on?
Lactobacillus iners, apparently my polished genome has just aligned to my reference genome
Dear Genome Projects, thank you very much for your video. I have tried to use mauve but I got an error (Exited with error code: -1073741819
).
Could I please get some help?
Greetings from Argentina
Ceci
Hi, not exactly sure about the error code.
Info on the web indicates this might be associated with Windows components needing an update. I would first try putting any files to align on your desktop and working from there - if they are not already. Also try only aligning a couple of genomes first (if you have a lot) in case the error relates to your memory availability for MAUVE to complete the tasks. You could also try "right click on MAUVE" and troubleshoot compatibility.
Hope this helps,
@@genomeprojects Thanks a lot for your answer! I´ll try that
Hi! I wanna ask, I already aligned 2 genome sequences and wanted to find a specific gene/product in the sequence navigator but still no results came out. Any suggestions or solutions? Thank you.
Might depend what is is annotated as in your reference genome. If you can find the gene in your GenBank file this will also give you a Locus Tag that you can search for in MAUVE rather than search for gene or product. You can also find the coordinates of the gene from your annotation file and then zoom into that region in MAUVE.
@@genomeprojects Okay thank you so much! Another question, if I put in 2 genomes how do I make 1 of them the reference genome?
@@cindyoctaviana9842
Your reference genome would normally be a complete genome I.e. a single annotated chromosome assembly - not a genome in numerous contigs.
When using progressive Mauve to align a genome to a reference, it is best to add the reference first - there is however an option to move the order of the genomes after the alignment has completed.
On the far left of the alignments there should be something that looks like:
^
-
R
V
You can use this to move the positions of the genomes and set which you want to use as a reference after alignment has completed.
@@genomeprojects sorry for the late reply, thank you so much for your help! it worked :)
did exact and got and error when i pressed align
Error in Mauve? I would check the file types you are using Genbank or FASTA etc.. as well as where you are saving the output files - in case there is a problem saving them to the location you have stated. Just a thought, I had issues once saving them to a USB.
@@genomeprojects My entire group is having problem where gb file gives an error. But when we only use fasta the program works fine
@@louismostert2650 if you are downloading the genome from NCBI - when on the page with the genome. In the "send to" drop down menu @ top of page, try selecting: complete record then select the destination as "file". Then in the drop down "format" options select GenBank (full) rather than just GenBank. Saving the file in this format has worked for me in the past.
Genome Projects wanna ask you some questions related to MAUVE if you available then answer me as soon as possible.
Sure, post a question and I will try and help.