# Sequence alignment parameters

**URL:** <https://forum.mothur.org/t/sequence-alignment-parameters/20674>\
**Category:** Commands in mothur\
**Created:** [September 6, 2020, 8:20am UTC](https://forum.mothur.org/t/sequence-alignment-parameters/20674 "2020-09-06T08:20:06Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![subbu](https://avatars.discourse-cdn.com/v4/letter/s/a88e57/32.png) [@subbu](https://forum.mothur.org/u/subbu)\
**Post date:** [September 6, 2020, 8:20am UTC](https://forum.mothur.org/t/sequence-alignment-parameters/20674/1 "2020-09-06T08:20:06Z")

</div>

Hi everyone, I have used V3-V4 region for amplicon sequencing to decipher insect gut mcirobiome . I am first time user of data science and learning concepts for microbiome data analysis. Kindly suggest me what would be the set parameters (Start and end) for aligning sequencing with Silva data base. The command for this step mentioned in Miseq-SOP manual is **mothur \> pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=8)**

**However, Miseq-SOP is based on V4 amplicon sequencing, I have done** V3-V4 region amplicon sequencing. What would be the ideal **start=?, end=? To execute the above said command?**  
primers used are  
Forward primer (5 -3 direction) GCCTACGGGNGGCWGCAG  
Reverse primer: (5 -3 direction): ACTACHVGGGTATCTAATCC  
Kindly help me out.

---

<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [September 9, 2020, 2:25pm UTC](https://forum.mothur.org/t/sequence-alignment-parameters/20674/2 "2020-09-09T14:25:08Z")

</div>

Hi there,

I’d encourage you to follow the [tutorial](https://mothur.org/blog/2016/Customization-for-your-region/) we posted for customizing the coordinates to your region of interest.

Thanks,  
Pat

---

<div class="post-metadata">

**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [September 19, 2020, 2:25pm UTC](https://forum.mothur.org/t/sequence-alignment-parameters/20674/3 "2020-09-19T14:25:20Z")

</div>

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.